Journal of Biochemistry - current issue

A Simple and Immediate Method for Simultaneously Evaluating Expression Level and Plasmid Maintenance in Yeast

2009-06-01

To allow the comprehensive assessments of yeast expression systems, a simple and immediate method for simultaneously evaluating the expression level and plasmid maintenance in yeast was demonstrated. This method uses green fluorescent protein (GFP) and flow cytometry (FCM) and is characterized by a dual analysis of the average intensity of GFP fluorescence and the population of GFP-expressing cells. The FCM analysis of GFP fluorescence intensity rapidly quantifies the expression level without complex manipulations, such as the enzymatic reaction of a lacZ reporter assay. Moreover, the single-cell analysis revealed that the proportion of cells expressing GFP in the cell cluster reflects the plasmid retention rate; therefore, the FCM analysis of the GFP-expressing population allows the immediate estimation of the plasmid retention rate without the 2- or 3-day incubation required for colony counting. We show that the FCM analysis with GFP reporter is a suitable method to explore the hopeful expression vector and host strain or establish the several expression systems exhibiting the characteristic properties in yeast.

Saccharomyces cerevisiae Na+/H+ Antiporter Nha1p Associates with Lipid Rafts and Requires Sphingolipid for Stable Localization to the Plasma Membrane

Mitsui, K., Hatakeyama, K., Matsushita, M., Kanazawa, H. — 2009-06-01

The plasma membrane-type Na⁺/H⁺ antiporter Nha1p from budding yeast plays an important role in intracellular Na⁺ and pH homeostasis by mediating the exchange of Na⁺ for H⁺ across the plasma membrane. However, the mechanism of intracellular targeting of Nha1p to the plasma membrane remains unknown. Here, we found that Nha1p exists predominantly in detergent-resistant membrane fractions (DRMs) following density gradient centrifugation. When ergosterol was extracted from membranes, Nha1p was transferred to a detergent-soluble fraction, suggesting that Nha1p associates with ergosterol-containing DRMs, also known as lipid rafts. Density gradient centrifugation of cell extracts of yeast mutants that were defective in different stages of the secretory pathway revealed that, unlike previously identified raft proteins, the association of Nha1p with DRMs occurs mainly at the plasma membrane. In lcb1-100 cells, which are temperature-sensitive for sphingolipid synthesis, newly synthesized Nha1p failed to localize to the plasma membrane at the non-permissive temperature. Rather, Nha1p was distributed in an intracellular punctate pattern. The addition of phytosphingosine or the inhibition of endocytosis in lcb1-100 cells restored the targeting of Nha1p to the plasma membrane. The results of the current study suggest that sphingolipids are required for the stable localization of Nha1p to the plasma membrane.

Guanidine Hydrochloride- and Urea-Induced Unfolding of Toxoplasma gondii Ferredoxin-NADP+ Reductase: Stabilization of a Functionally Inactive Holo-Intermediate

Singh, K., Bhakuni, V. — 2009-06-01

Usually during the folding/unfolding of flavoproteins, an apo-intermediate is stabilized before global unfolding of the enzymes occurs. However, stabilization of a holo-intermediate has also been reported for a few flavoproteins. We have studied the unfolding of Toxoplasma gondii ferredoxin-NADP⁺ reductase (TgFNR) using GdnHCl and urea. A functionally inactive holo-intermediate of the enzyme was found to be stabilized during this unfolding process. The intermediate species had cofactor FAD bound to it, but it showed free movement due to which the stabilized intermediates were functionally inactive. The native TgFNR behaves cooperatively with the two structural domains interacting strongly with each other. The denaturants GdnHCl and urea, at low concentrations, were found to interact selectively with the NADP⁺-binding domain of TgFNR and to induce structural modifications in it. These selective modifications in the protein molecule lead to loss of interactions between two domains and the enzyme behaved non-cooperatively resulting in stabilization of an intermediate species. Significant differences in the structural properties of the GdnHCl- and urea-stabilized holo-intermediates of TgFNR were observed. Comparison of the unfolding pathway of TgFNR (a plant-type FNR) with that of FprA (a GR-type FNR) demonstrates that they follow very different pathways of unfolding.

Post-Transcriptional Regulation of the Expression of Ferrochelatase by Its Variant mRNA

Sakaino, M., Kataoka, T., Taketani, S. — 2009-06-01

Ferrochelatase (FECH) catalyses the insertion of ferrous ions into protoporphyrin IX to produce haem at the haem-biosynthetic pathway. The present study characterized a variant mRNA of mouse FECH, which was generated by skipping exon II (FECH-v). FECH-v mRNA was expressed in various tissues, including the liver and kidney, of mice. The mRNA was also expressed in mouse and human non-erythroid and erythroid cells to a different extent but could not be translated into functional FECH. The ratio of FECH-v/FECH increased in hemin-treated Balb/3T3 cells, while it decreased after treatment with succinylacetone, an inhibitor of haem biosynthesis, strongly suggesting that FECH expression was decreased by increasing the level of intracellular haem. These results demonstrated the haem-dependent negative feedback regulation of the expression of FECH at a post-transcriptional level.

Evaluation of Conditions for Release of Mucin-Type Oligosaccharides from Glycoproteins by Hydrazine Gas Treatment

Goso, Y., Tsubokawa, D., Ishihara, K. — 2009-06-01

By using commercially available anhydrous hydrazine in the gas-phase, mucin-type oligosaccharides were released from porcine gastric mucin (PGM) and bovine fetuin. The data indicated that a certain amount of the oligosaccharides from PGM were further degraded. Despite this, the HPLC elution profile of the anthranilic acid (AA)-derivatized oligosaccharides obtained by the treatment with hydrazine at 65°C for 6 h resembled those obtained from the alkaline-borohydride treatment, except for the additional disaccharide fractions derived from the core 1 side of the oligosaccharides by further degradation. The other degraded products derived from the core 2 side could not be derivatized by AA, therefore, not visible by fluorescence detection. Liberation of the oligosaccharides was incomplete by the hydrazine treatment for 6 h. Although almost complete liberation was achieved by extending the treatment to 18 h, the degraded products also increased. In this case, the addition of barium oxide to the reaction vessel decreased the degree of further degradation. Results similar to PGM were obtained from bovine fetuin, but with less degradation. Application of this method for the analysis of rat gastric mucin (RGM) obtained from the corpus and antral region revealed that RGM has a large oligosaccharide portion on the core 1 side.

Sequence Perturbation Analysis: Addressing Amino Acid Indices to Elucidate the C-Terminal Role of Escherichia Coli Dihydrofolate Reductase

Takahashi, H., Yokota, A., Takenawa, T., Iwakura, M. — 2009-06-01

Because amino acid residues intrinsically possess many factors participating in protein structures and functions, to determine main (or unique) factors at a specific site in a protein sequence should be of great help for understanding how a protein obtains its structure and function. In this study, we proposed a means of sequence perturbation analysis to address the above concerns involving comprehensive AA indices. We constructed all 19 possible single mutant proteins as to the three sites in the C-terminal of Escherichia coli dihydrofolate reductase (DHFR), and measured the activity and thermal stability of each of all the single mutant proteins. The significantly perturbed properties with each systematic single mutation at each mutational site were examined in terms of the linear correlation with each AA index. As a result, at each of Arg158 and Arg159 of DHFR, the AA index for the isoelectric points of amino acids showed strong correlation with the transition temperature of thermal denatuation, suggesting that the electrostatic interaction is the main factor influencing the C-terminal role of the DHFR. The feasibility and general versatility of our sequence perturbation analysis were also examined by application to other sites of DHFR.

Probing the haem d-binding site in cytochrome bd quinol oxidase by site-directed mutagenesis

Mogi, T. — 2009-06-01

Cytochrome bd is a cyanide-resistant terminal quinol oxidase under micro-aerophilic growth conditions and generates a proton motive force via scalar protolytic reactions. Protons used for dioxygen reduction are taken up from the cytoplasm and delivered to haem d through a proton channel. Electrons are transferred from quinols to haem d through haem b₅₅₈ and haem b₅₉₅. All three haems are bound to subunit I but only the axial ligand of haem d remains to be determined. Haems b₅₉₅ and d form a haem–haem binuclear centre and substitutions of either His19 in helix I (haem b₅₉₅ ligand) and Glu99 in helix III eliminated or severely reduced both haems. To probe the location of the haem d ligand, we introduced mutations around His19 and Glu99 and examined the cyanide-resistance of the oxidase activity and spectroscopic properties. In contrast to mutations around His19, I98F and L101T reduced the IC₅₀ for cyanide to 0.18 and 0.41 mM, respectively, from 1.4 mM of the wild-type. Blue shifts in the peak of I98F suggest that Ile98 is in the vicinity of the haem d-binding site. Our data are consistent with the proposal that Glu99 serves as a haem d ligand of cytochrome bd.

Simvastatin Suppresses Leptin Expression in 3T3-L1 Adipocytes via Activation of the Cyclic AMP-PKA Pathway Induced by Inhibition of Protein Prenylation

Maeda, T., Horiuchi, N. — 2009-06-01

Simvastatin inhibits 3-hydroxy-3-methylglutaryl-coenzyme A (HMG-CoA) reductase, which catalyses conversion of HMG-CoA to mevalonate, a rate-limiting step in cholesterol synthesis. We demonstrated that simvastatin at 1 µM markedly inhibited adipocyte differentiation measured by Oil Red O staining in preadipocyte cells (3T3-L1), while expression of leptin, a marker of adipocyte differentiation, was suppressed by 1 µM simvastatin for up to 12 days of culture. Next, to elucidate mechanisms underlying the reduction of leptin expression induced by simvastatin, differentiated 3T3-L1 adipocytes were treated with various inhibitors with mevalonate or its metabolite in the presence or absence of simvastatin. Simvastatin time- and dose-dependently suppressed leptin mRNA expression. Heterogeneous nuclear RNA related to leptin mRNA was inhibited by 10 µM simvastatin, while stability of the mRNA was not changed by treatment with simvastatin in transcription-arrested 3T3-L1 cells. Simvastatin inhibition of leptin gene transcription was not abrogated by pre-treatment with cycloheximide, an inhibitor of protein synthesis. Addition of mevalonate or geranylgeranyl pyrophosphate (GGPP), a mevalonate metabolite, abolished simvastatin-induced inhibition of leptin expression in 3T3-L1 cells. Suppression of expression was observed upon addition of GGTI-298, a geranylgeranyl transferase I inhibitor, but not FTI-277, a farnesyl transferase inhibitor. Expression was suppressed by treatment with hydroxyfasudil, a protein prenylation inhibitor. Treatment with phosphatidylinositol 3-kinase (PI3K) inhibitors, LY294002 and wortmannin, reduced leptin expression in 3T3-L1 cells. Simvastatin dose-dependently increased intra-cellular cyclic AMP (cAMP) concentrations in 3T3-L1 cells, with maximal stimulation obtained at 10 µM. Addition of GGPP abolished simvastatin-induced stimulation of cAMP accumulation and protein kinase A (PKA) activity. H89, an inhibitor of PKA, completely abolished simvastatin-induced suppression of leptin expression. These results suggested that simvastatin reduced geranylgeranylprotein prenylation followed by deactivation of PI3K, leading to cAMP accumulation and subsequent activation of PKA in differentiated 3T3-L1 adipocytes. Finally, PKA inhibited leptin gene transcription without new protein synthesis.

Role of the Stem Domain of Matriptase in the Interaction with its Physiological Inhibitor, Hepatocyte Growth Factor Activator Inhibitor Type I

Kojima, K., Tsuzuki, S., Fushiki, T., Inouye, K. — 2009-06-01

Matriptase is a type II transmembrane serine protease containing the non-catalytic domains (stem domain) and catalytic domain in the extra-cellular region. Our aim is to address the role of the stem domain in the interaction between matriptase and its physiological inhibitor, hepatocyte growth factor activator inhibitor type I (HAI-1). We prepared secreted variants of recombinant matriptase containing the entire extra-cellular domain (HL-matriptase) or only the catalytic domain (L-matriptase), and compared the inhibition activities of a cell membrane-anchored form of recombinant HAI-1 (maHAI-1) against the matriptase variants in the hydrolysis of peptidyl–4-methyl-coumaryl-7-amide (MCA) substrates. HL-matriptase and L-matriptase were inhibited by purified maHAI-1 with a similar extent when t-butyloxycarbonyl (Boc)-Gln-Ala-Arg-MCA (1) and acetyl-Lys-Thr-Lys-Gln-Leu-Arg-MCA (2) were used as substrates. However, HL-matriptase was inhibited more strongly than L-matriptase by maHAI-1 in the hydrolysis of Boc-[(2S)-2-amino-3-(benzyloxycarbonyl)propionyl]-Pro-Arg-MCA (3). These results show that the stem domain of matriptase facilitates the inhibitory interaction of this protease with maHAI-1 in the hydrolysis of substrate 3, although it has no effect in the hydrolysis of substrates 1 and 2. To our knowledge, this is the first evidence that the stem domain of matriptase can affect the interaction between this protease and HAI-1.

Comparison of Total Protein Concentration in Skeletal Muscle as Measured by the Bradford and Lowry Assays

Seevaratnam, R., Patel, B. P., Hamadeh, M. J. — 2009-06-01

The Lowry and Bradford assays are the most commonly used methods of total protein quantification, yet vary in several aspects. To date, no comparisons have been made in skeletal muscle. We compared total protein concentrations of mouse red and white gastrocnemius, reagent stability, protein stability and range of linearity using both assays. The Lowry averaged protein concentrations 15% higher than the Bradford with a moderate correlation (r = 0.36, P = 0.01). However, Bland–Altman analysis revealed considerable bias (15.8 ± 29.7%). Both Lowry reagents and its protein–reagent interactions were less stable over time than the Bradford. The linear range of concentration was smaller for the Lowry (0.05–0.50 mg/ml) than the Bradford (0–2.0 mg/ml). We conclude that the Bradford and Lowry measures of total protein concentration in skeletal muscle are not interchangeable. The Bradford and Lowry assays have various strengths and weaknesses in terms of substance interference and protein size. However, the Bradford provides greater reagent stability, protein–reagent stability and range of linearity, and requires less time to analyse compared to the Lowry assay.

Effective Induction of Cell Death on Adult T-Cell Leukaemia Cells by HLA-DR{beta}-Specific Small Antibody Fragment Isolated from Human Antibody Phage Library

2009-06-01

By a biopanning method using cell sorter, we quickly isolated an antibody phage clone (S1T-A3) specific to human T-lymphotropic virus type 1-carrying T-cell line S1T from a human single chain Fv (scFv) antibody phage library. This scFv antibody bound to HTLV-1-carrying T-cell lines including MT-2, MT-4 and M8166 other than S1T, but not to non-HTLV-1-carrying T-cell lymphomas such as Jurkat and MOLT4 cells. Interestingly, this antibody induced the cell death on S1T cells very quickly (< 30 min). We tried to identify the target molecules by western blotting and mass spectrometric analysis, revealing that the target antigen was HLA class II DR. The cell death was induced only in dimmer form of scFv (diabody) and at 15-fold lower concentration than that of a fusion protein of scFv and human IgG Fc [(scFv)₂-Fc] or anti HLA-DR mouse whole antibody L243. Thus, S1T-A3 diabody is a small antibody fragment with agonistic activity to induce cell death through HLA-DR. This is the first report elucidating that diabody specific to HLA-DR is effective to induce the cell death in T-cell malignancy especially adult T-cell leukaemic cell line.

Isolation of ON Bipolar Cell Genes via hrGFP-coupled Cell Enrichment Using the mGluR6 Promoter

Nakajima, Y., Moriyama, M., Hattori, M., Minato, N., Nakanishi, S. — 2009-06-01

mGluR6 expression is a characteristic property of retinal ON bipolar cells. mGluR6 is also the causal gene for a form of congenital night blindness. To elucidate physiological and pathological functions of ON bipolar cells and mGluR6, we thought it important to identify genes specifically expressed in them. We thus made transgenic mouse lines expressing humanized Renilla reniformis green fluorescent protein (hrGFP), under the control of the mGluR6 promoter. From their retina, we isolated hrGFP-positive cells by cell sorting, and analysed the gene-expression profile of these cells by using DNA microarray. Further analysis revealed that about half of the initially selected ON bipolar cell genes were expressed in the expected retinal layer. We confirmed previously ambiguous retinal localization of regulator of G-protein signalling 11 (RGS11) and transient receptor potential cation channel, subfamily M, member 1 (TRPM1). In addition, we showed the expression of calcium channel, voltage-dependent, alpha2/delta subunit 3 (Cacna2d3) in ON bipolar cells for the first time. Although we could not completely exclude the possibility that a small population of hrGFP-positive cells might not be ON bipolar cells, these mice as well as our strategy would be highly valuable for the further analysis of ON bipolar cells.