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Lumbar cerebrospinal fluid proteome in multiple sclerosis: characterization by ultrafiltration, liquid chromatography, and mass spectrometry.

Neurological diseases, including multiple sclerosis (M.S.), often provoke changes in the functioning of the endothelial and epithelial brain barriers and give rise to disease-associated alterations of the cerebrospinal fluid (CSF) proteome. In the present study, pooled and ultrafiltered CSF of M.S. and non-M.S. patients was digested with trypsin and analyzed by off-line strong cation-exchange chromatography (SCX) coupled to on-line reversed-phase LC-ESI-MS/MS. In an alternative approach, the trypsin-treated subproteomes were analyzed directly by LC-ESI-MS/MS and gas-phase fractionation in the mass spectrometer. Taken together, both proteomic approaches in combination with a three-step evaluation process including the search engines Sequest and Mascot, and the validation software Scaffold, resulted in the identification of 148 proteins. Sixty proteins were identified in CSF for the first time by mass spectrometry. For validation purposes, the concentration of cystatin A was determined in individual CSF and serum samples of M.S. and non-M.S. patients using ELISA.

Adult↗

Hypovirulence: mycoviruses at the fungal-plant interface.

Whereas most mycoviruses lead 'secret lives', some reduce the ability of their fungal hosts to cause disease in plants. This property, known as hypovirulence, has attracted attention owing to the importance of fungal diseases in agriculture and the limited strategies that are available for the control of these diseases. Using one pathogen to control another is appealing, both intellectually and ecologically. The recent development of an infectious cDNA-based reverse genetics system for members of the Hypoviridae mycovirus family has enabled the analysis of basic aspects of this fascinating virus-fungus-plant interaction, including virus-host interactions, the mechanisms underlying fungal pathogenesis, fungal signalling pathways and the evolution of RNA silencing. Such systems also provide a means for engineering mycoviruses for enhanced biocontrol potential.

Ascomycota↗

A key amino acid responsible for substrate selectivity of monoamine oxidase A and B.

Monoamine oxidase (MAO) oxidizes biologically important amines including neurotransmitters and plays a central role in the regulation of intracellular level of these amines. Two distinct forms of MAO (MAO A and MAO B) were defined based on differences in substrate and inhibitor specificities. We earlier reported that the region between about residues 120 and 220 of rat MAO is responsible for determination of the substrate selectivity of MAO A and B (Tsugeno, Y. Hirashiki, I., Ogata, F., and Ito, A. (1995) J. Biochem. (Tokyo) 118, 974-980). To determine the essential amino acids in this region that participate in substrate recognition, a series of mutant enzymes in which amino acid residues that are conserved among various species but are different between the two forms of the enzyme were replaced with the corresponding amino acids of the counterpart and were engineered from the cDNAs of rat liver MAO A and B, and affinities for several substrates were examined. A single mutation in which Phe-208 in MAO A was substituted by the corresponding residue of Ile in MAO B was sufficient to convert the A-type substrate selectivity, and the reverse was exactly the case. Phe at this position was replaceable with Tyr for the A-type specificity and Ile was replaceable with Val and Ala for the B-type. Thus, aromatic and aliphatic residues seem to contribute to render substrate selectivity of MAO A and MAO B, respectively.

Amino Acid Sequence↗

pH-induced conformational changes of AcrA, the membrane fusion protein of Escherichia coli multidrug efflux system.

The multidrug efflux system AcrA-AcrB-TolC of Escherichia coli expels a wide range of drugs directly into the external medium from the bacterial cell. The mechanism of the efflux process is not fully understood. Of an elongated shape, AcrA is thought to span the periplasmic space coordinating the concerted operation of the inner and outer membrane proteins AcrB and TolC. In this study, we used site-directed spin labeling (SDSL) EPR (electron paramagnetic resonance) spectroscopy to investigate the molecular conformations of AcrA in solution. Ten AcrA mutants, each with an alanine to cysteine substitution, were engineered, purified, and labeled with a nitroxide spin label. EPR analysis of spin-labeled AcrA variants indicates that the side chain mobilities are consistent with the predicted secondary structure of AcrA. We further demonstrated that acidic pH induces oligomerization and conformational change of AcrA, and that the structural changes are reversible. These results suggest that the mechanism of action of AcrA in drug efflux is similar to the viral membrane fusion proteins, and that AcrA actively mediates the efflux of substrates.

Alanine↗

Functional difference between the two oppositely oriented priming signals essential for the initiation of the broad host-range plasmid RSF1010 DNA replication.

The broad host-range plasmid RSF1010 contains two oppositely oriented priming signals, ssiA and ssiB, for DNA synthesis dependent on the origin of vegetative DNA replication (oriV). If either ssiA or ssiB was deleted or inverted, the RSF1010 miniplasmids containing engineered oriVs were maintained at low copy numbers, replicated abnormally as dimers, and accumulated specific single strands in the Escherichia coli strain supplying the three RSF1010-encoded RepA, RepB', and RepC proteins. Interestingly, an additional intracellular supply of the Sog primase (the sog gene product of plasmid CoIIb-P9) reversed the replication deficiency of these miniplasmids with respect to all three aspects described above. These were also true for the RSF1010 miniplasmids in which either ssiA or ssiB was replaced by the primosome assembly site (PAS) or by the G4-type ssi signal (G site). Furthermore, comparative analysis of the functional contribution of the two oppositely oriented ssi signals to the DNA replication of RSF1010 showed that, irrespective of their types, ssi signals conducting the initiation of DNA chain elongation away from the iterons were functionally more important than ones in the inverted orientation. We consider that this functional difference reflects the inherent properties of the initiation mechanism of RSF1010 DNA replication.

Bacterial Proteins↗

Engineering and functional evaluation of a single-chain antibody against HIV-1 external glycoprotein gp120.

The HIV-1 envelope glycoprotein surface subunit gp120 is an attractive target for molecular intervention. This is because anti-HIV-1 gp120 neutralizing antibodies display the potential ability to inhibit HIV-1 infection. The present investigation describes the construction of a genetically engineered single chain antibody (scFv102) against HIV-1 gp120, its expression and functional evaluation. The parental hybridoma cell line (102) produces an immunoglobulin directed against the conserved CD4-binding region of gp120. cDNAs encoding the variable regions of the heavy (V(H)) and light (V(L)) chains were prepared by reverse transcription PCR and linked together with an oligonucleotide encoding a linker peptide (Gly(4)Ser)(3) to produce a single chain antibody gene. The resulting DNA construct was cloned into a prokaryotic expression vector (pET28) and recombinant scFv102 was expressed in Eserichia coli as an insoluble protein. The denatured scFv102 was refolded and purified by immobilized metal ion affinity chromatography. Purified scFv102 had the same specificity as the intact IgG in immuno-blotting assays and immuno-fluorescence (IF) detection, but ELISA analyses demonstrated the affinity of scFv102 to be 5-fold lower than that of the parental monoclonal antibody. In neutralization assays, scFv102 at concentrations lower than 40 microg/ml exhibited efficient interference with viral replication and inhibition of viral infection (90%) across a range of primary isolates of subtype B HIV-1. These results suggest that the constructed anti-HIV-1 gp120 scFv102 has good biological activity and can potentially be used for in vitro diagnostic and in vivo therapeutic applications.

Amino Acid Sequence↗

Excretion of human beta-endorphin into culture medium by using outer membrane protein F as a fusion partner in recombinant Escherichia coli.

Escherichia coli BL21 strains were found to excrete a large amount of outer membrane protein F (OmpF) into culture medium during high-cell-density cultivation. From this interesting phenomenon, a novel and efficient OmpF fusion system was developed for the excretion of recombinant proteins by E. coli. The ompF gene of E. coli BL21(DE3) was first knocked out by using the red operon of bacteriophage lambda to construct E. coli MBEL-BL101. For the excretion of human beta-endorphin as a model protein, the beta-endorphin gene was fused to the C terminus of the E. coli ompF gene by using a linker containing the Factor Xa recognition site. To develop a fed-batch culture condition that allows efficient production of OmpF-beta-endorphin fusion protein, three different feeding strategies, an exponential feeding strategy and two pH-stat strategies with defined and complex nutrient feeding solutions, were examined. Among these, the pH-stat feeding strategy with the complex nutrient feeding solution resulted in the highest productivity (0.33 g of protein per liter per h). Under this condition, up to 5.6 g of OmpF-beta-endorphin fusion protein per liter was excreted into culture medium. The fusion protein was purified by anion-exchange chromatography and cleaved by Factor Xa to yield beta-endorphin, which was finally purified by reverse-phase chromatography. From 2.7 liters of culture supernatant, 545.4 mg of beta-endorphin was obtained.

Bacterial Outer Membrane Proteins↗

A nucleotide substitution in the tRNA(Lys) primer binding site dramatically increases replication of recombinant simian immunodeficiency virus containing a human immunodeficiency virus type 1 reverse transcriptase.

A recombinant simian immunodeficiency virus (SIV) derived from strain 239 (SIVmac239) with reverse transcriptase (RT) sequences from human immunodeficiency virus type 1 (HIV-1) strain HXB2 was severely impaired for replication. Detectable p27(Gag) levels were not observed until day 65 and peak p27(Gag) levels were not reached until day 75 after transfection of CEMx174 cells with the recombinant DNA. Sequences from the latter time point did not contain amino acid substitutions in HIV-1 RT; however, a single nucleotide substitution (thymine to cytosine) was found at position eight of the SIV primer binding site. We engineered an RT/SHIV genome with the thymine-to-cytosine substitution, called RT/SHIV/TC, and observed dramatically faster replication kinetics than were observed with the parental RT/SHIV from which this variant was derived. RT/SHIV/TC provides an improved system for study of the impact of drug resistance mutations in HIV-1 RT in a relevant animal model.

Amino Acid Substitution↗

Health effects of occupational exposure to acrylamide using hemoglobin adducts as biomarkers of internal dose.

OBJECTIVES: This study assessed the health effects of occupational acrylamide exposure using hemoglobin (Hb) adducts as biomarkers of internal dose. METHODS: Two hundred and ten tunnel workers exposed for about 2 months to a chemical-grouting agent containing acrylamide and N-methylolacrylamide underwent a health examination. Blood samples were drawn for the analysis of Hb adducts of acrylamide. Fifty workers claiming recently developed or deteriorated symptoms of the peripheral nervous system (PNS) were referred to a neurophysiological examination. Workers with Hb-adduct levels exceeding 0.3 nmol/g globin attended follow-up examinations 6, 12, and 18 months after exposure cessation. RESULTS: Forty-seven workers had Hb-adduct levels within the normal background range (0.02-0.07 nmol/g globin), while the remaining 163 had increased levels up to a maximum of 17.7 nmol/g globin. Clear-cut dose-response associations were found between the Hb-adduct levels and PNS symptoms. Thirty-nine percent of those with Hb-adduct levels exceeding 1 nmol/g globin experienced tingling or numbness in their hands or feet. A no-observed adverse effect level of 0.51 nmol/g globin was estimated for numbness or tingling in the feet or legs. For 23 workers there was strong evidence of PNS impairment due to occupational exposure to acrylamide. All but two had recovered 18 months after the cessation of exposure. CONCLUSIONS: Occupational exposure to a grouting agent containing acrylamide resulted in PNS symptoms and signs. The use of Hb adducts of acrylamide as a biomarker of internal dose revealed strong dose-response associations. The PNS symptoms were, however, generally mild, and in almost all cases they were reversible.

Acrylamide↗

Biological equivalence of natural bovine and recombinant human alpha-endothelial cell growth factors.

The cDNA encoding human alpha-endothelial cell growth factor (alpha-ECGF) has been engineered for high-level expression in Escherichia coli. Induction of bacterial cultures harboring the recombinant plasmid pMJ26 results in the appearance of a prominent 16-kDa polypeptide. This protein has been purified from bacterial lysates using a rapid, 2-step procedure employing heparin-Sepharose affinity based chromatography and reversed-phase high pressure liquid chromatography. Recombinant human alpha-ECGF was compared to bovine brain-derived alpha-ECGF in three biological assays: receptor binding on murine lung capillary endothelial cells (LE-II cells), stimulation of [3H]thymidine incorporation in LE-II cells, and stimulation of human umbilical vein endothelial cell proliferation. The results demonstrate that the recombinant human mitogen has the same biological potency as the bovine brain-derived material. Fluorescence spectroscopy was used to study the interaction between recombinant ECGF and heparin. Heparin-binding resulted in a 40% reduction in the intrinsic fluorescence of ECGF, consistent with a heparin-induced conformational change. The intrinsic fluorescence of ECGF also varied as a function of pH.

Amino Acids↗

GMAP: a multi-purpose computer program to aid synthetic gene design, cassette mutagenesis and the introduction of potential restriction sites into DNA sequences.

A computer program called GMAP has been developed for i) mapping the potential restriction endonuclease (R.E.) sites that can be introduced in a nonambiguous DNA sequence; ii) predicting the mutations required to introduce unique R.E. sites in the nonambiguous DNA sequences; and iii) searching all R.E. sites in ambiguous DNA sequence obtained by reverse translation of a given amino acid sequence. This allows the design of synthetic genes as well as the modular redesign after introducing limited base pair mismatches in wild-type genes in order to adapt them for "cassette" mutagenesis. The GMAP program uses an algorithm based on set theory that reduces the degree of complexity from an exponential to linear function of sequence length. Therefore, the speed of searching for potential R.E. sites in reverse-translated gene sequences and the prediction of new R.E. sites in natural genes by mutations are rapid.

Algorithms↗

[Contributions and prospects of hemoglobin derivatives].

Anoxia-reoxygenation leads to severe metabolic alterations, which result in a generalized inflammatory reaction and multiple organ dysfunction. Direct blood transfusion limits these alterations, but is accompanied by risk of transmission of infections or viral diseases. To avoid these risks, "blood substitutes" have been designed. The modified hemoglobins are not true blood substitutes because they do not possess the complex functions of erythrocytes. They are only oxygen carriers, with a short intravascular life, adapted for temporary use. They are stable, devoid of toxicity and antigenicity, and are able to carry and deliver O2 without regulation of this oxygen transport and without chemical reaction with O2. They possess rheologic properties and an oncotic pressure like those of blood. The use of natural hemoglobin solutions, obtained after lysis of erythrocytes, remains "at risk" because these solutions easily form methemoglobin, increase the oncotic pressure, present renal toxicity, and possess a too high affinity for O2. For these reasons, 5 types of modified hemoglobin solutions have been designed, prepared from human or bovine hemoglobin or by genetic engineering. These hemoglobins are highly purified to eliminate trace amounts of stroma, lipids and endotoxins, which are responsible for acute toxicity. They are modified by internal cross-linking between the monomers, or by binding to macromolecules. Afterwards, they can be polymerized or encapsulated in liposomes. The purpose of these modifications is to modulate the affinity for O2 (by decreasing the binding of O2 and increasing its delivery to tissue), to reduce the dissociation into monomers and to guard against oxidation into methemoglobin. Encapsulation in liposomes allows co-encapsulation of effector molecules and protective substances. Genetic engineering allows the production of recombinant hemoglobin with selective modifications. The modified hemoglobin solutions are essentially used in hemorrhagic shock and perioperative hemodilution. Experimental work in animals has afforded good results: restoration of normal O2 pressure and no toxicity. These assays allow frequent observation of an unexpected rapid hypertensive effect, transient, reversible, and that could be controlled by antihypertensive drugs. The mechanisms of this hypertensive effect remain controverted (stimulation of endothelin production, inhibition of nitric oxide effects, etc.). In humans, studies with healthy volunteers have been completed, while phase II clinical studies are under way in hypovolemic shock, in major abdominal, orthopedic and cardiac surgery, in stroke and in intensive care patients after surgery. The detailed results are awaited, but the modified hemoglobin solutions already appear to be without toxicity and present the same hypertensive effect as observed in animals. However, until now only low doses have been used, and the catabolism of these solutions remains largely unknown.

Animals↗

A comparative analysis of the plant cellulose synthase (CesA) gene family.

CesA genes are believed to encode the catalytic subunit of cellulose synthase. Identification of nine distinct CesA cDNAs from maize (Zea mays) has allowed us to initiate comparative studies with homologs from Arabidopsis and other plant species. Mapping studies show that closely related CesA genes are not clustered but are found at different chromosomal locations in both Arabidopsis and maize. Furthermore, sequence comparisons among the CesA-deduced proteins show that these cluster in groups wherein orthologs are often more similar than paralogs, indicating that different subclasses evolved prior to the divergence of the monocot and dicot lineages. Studies using reverse transcriptase polymerase chain reaction with gene-specific primers for six of the nine maize genes indicate that all genes are expressed to at least some level in all of the organs examined. However, when expression patterns for a few selected genes from maize and Arabidopsis were analyzed in more detail, they were found to be expressed in unique cell types engaged in either primary or secondary wall synthesis. These studies also indicate that amino acid sequence comparisons, at least in some cases, may have value for prediction of such patterns of gene expression. Such analyses begin to provide insights useful for future genetic engineering of cellulose deposition, in that identification of close orthologs across species may prove useful for prediction of patterns of gene expression and may also aid in prediction of mutant combinations that may be necessary to generate severe phenotypes.

Arabidopsis↗

Genetically engineered elastin-protein A fusion as a universal platform for homogeneous, phase-separation immunoassay.

A simple and universal platform for competitive phase-separation immunoassay is reported based on a fusion protein composed of a temperature-responsive elastin-like polypeptide (ELP) and the antibody-binding staphylococcal protein A (SpA). The basic principle is to take advantage of the ability of SpA to bind a variety of antibodies with high affinity, allowing simple separation of antigen-antibody complex by thermal precipitation. The resulting ELP-SpA fusion was shown to preserve the ability to reversibly precipitate as well as its high affinity toward different IgGs and IgMs. As a model system, a competitive phase-separation immunoassay based on the ELP-SpA format was established for paclitaxel (taxol) with IC(50) (20.18 nM) and the lower detection limit (2.94 nM) very similar to those reported for the ELISA format. Unlike the heterogeneous interaction in ELISA, which decreases the antibody-binding activity, the reported homogeneous immunoassay not only alleviates this problem but also enables the potential for high-throughput automation. We believe that the reported ELP-SpA fusion will find applications not only as a powerful diagnostic tool for diverse analytes but also a potential useful tool for purification and immobilization of antibody.

Elastin↗

Hydrophobic displacement chromatography of proteins.

Displacement chromatography of proteins was successfully carried out in both hydrophobic interaction and reversed-phase chromatographic systems using low-molecular weight displacers. The displacers employed for hydrophobic displacement chromatography were water soluble, charged molecules containing several short alkyl and/or aryl groups. Spectroscopy was employed to verify the absence of structural changes to the proteins displaced on these hydrophobic supports. Displacement chromatography on a reversed-phase material was employed to purify a growth factor protein from its closely related variants, demonstrating the high resolutions that can be achieved by hydrophobic displacement chromatography. This process combines the high-resolution/high-throughput characteristics of displacement chromatography with the unique selectivity of these hydrophobic supports and offers the chromatographic engineer a powerful tool for the preparative purification of proteins.

Biotechnology↗

In vitro induction of adult hepatic progenitor cells into insulin-producing cells.

Organ-specific stem cells are the natural progenitors in tissue regeneration and possess plasticity to differentiate into specialized cells in adult tissues. Small hepatocytes (SHCs) identified in the adult liver are one such cell type. Here we show that SHCs, which are capable of self-renewal and differentiation into hepatocytes, can be induced to generate insulin-producing cells under appropriate culture conditions. These differentiated cells express pancreatic beta cell differentiation-related transcripts and hepatocyte differentiation-related transcripts, as shown by reverse-transcription PCR/nested PCR. In addition, enforced expression of the homeodomain transcription factor Pdx1 in these cells contributes to enhancement of insulin release in response to insulin secretagogues. These results indicate that the SHCs described here have the ability to differentiate into insulin-producing cells, and further support the idea that engineering to generate insulin-secreting cells could provide a useful resource for future therapies for diabetes mellitus.

Animals↗

Stable production of a human growth hormone antagonist from CHO cells adapted to serum-free suspension culture.

Human growth hormone (hGH) is a polypeptide with 191 amino acids and a molecular mass of 22 kDa. An hGH analogue was created with a single amino acid substitution (glycine[G] 120 to arginine[R]) in the third alpha-helix of the hGH molecule. This hGH analogue, named hGHG120R, was found to be an hGH antagonist. It is a parenteral drug candidate for treating conditions in which hGH levels are abnormally high, as found in type I diabetics. Previously, a genetically engineered anchorage-dependent mouse L cell line was created that produced and secreted hGHG120R in culture media (Dulbecco's modified Eagle's medium, DMEM) supplemented with 5% NuSerum IV. A multistep downstream process was developed to purify hGHG120R. The process consisted of cell clarification, salt precipitation, membrane ultrafiltration, size exclusion chromatography, reversed phase high-performance liquid chromatography, phase separation, and lyophilization. Here, we present the development of a superior eukaryotic system using a proper combination of genetic elements, cell line, and media formulation. This system is suitable for the large-scale production of the recombinant protein and is superior to the previously developed system in that it increases the specific production rate and at the same time eases the burden of the purification process, in both time and efficiency. Dihydrofolate reductase mutant (DHFR-) Chinese hamster ovary (CHO) cells were used that were stably transfected with an expression vector in which the hGHG120R gene is driven by the relatively strong human cytomegalovirus-early gene regulatory region. The hGHG120R tested to be biologically active. These cells were then adapted to grow in suspension in CHO-S-SFM (serum-free media). High cell densities, typically 2.0 x 10(6) cells/mL were obtained from spinner flask cultures. Partial purification of hGHG120R from CHO cell cultured media revealed that the level of impurities in SFM was significantly lower than the serum-supplemented DMEM. This suggests that the salt precipitation and the SEC step need not be employed in the purification of hGHG120R from SFM. This would result in a reduction of the operating time by 50 h and boost the recovery yield of hGHG120R to 75%.

Adaptation, Physiological↗

Substantial increase of protein stability by multiple disulphide bonds.

Disulphide bonds can significantly stabilize the native structures of proteins. The effect is presumed to be due mainly to a decrease in the configurational chain entropy of the unfolded polypeptide. In phage T4 lysozyme, a disulphide-free enzyme, engineered disulphide mutants that crosslink residues 3-97, 9-164 and 21-142 are significantly more stable than the wild-type protein. To investigate the effect of multiple-disulphide bonds on protein stability, mutants were constructed in which two or three stabilizing disulphide bridges were combined in the same protein. Reversible thermal denaturation shows that the increase in melting temperature resulting from the individual disulphide bonds is approximately additive. The triple-disulphide variant unfolds at a temperature 23.4 degrees C higher than wild-type lysozyme. The results demonstrate that a combination of disulphide bonds, each of which contributes to stability, can achieve substantial overall improvement in the stability of a protein.

DNA Mutational Analysis↗