Structure-Based Phylogenies of the Serine β-Lactamases

The serine -lactamases present a special problem for phylogenetics because they have diverged so much that they fall into three classes that share no detectable sequence homology among themselves. Here we offer a solution to the problem in the form of two phylogenies that are based on a protein structure alignment. In the first, structural alignments were used as a guide for aligning amino acid sequences and in the second, the average root mean square distances between the alpha carbons of the proteins were used to create a pairwise distance matrix from which a neighbor-joining phylogeny was created. From those phylogenies, we show that the Class A and Class D -lactamases are sister taxa and that the divergence of the Class C -lactamases predated the divergence of the Class A and Class D -lactamases.     

Supersensitivity to β-Lactam Antibiotics in Escherichia coli Caused by D-Alanine Carboxypeptidase IA Mutation

Escherichia coli cells acquired supersensitivity to various β-lactam antibiotics by dacA mutation, a defect in D-alanine carboxypeptidase IA activity. The mutant cells were rather less sensitive to mecillinam than the dacA⁺ cells. This mutation did not result in either thermosensitivity of cell growth or appreciable increase of the generation times in usual rich media, but the resulting appearance of supersensitivity to β-lactam antibiotics suggests that the cell wall or envelope of this mutant is somewhat abnormal and thus that D-alanine carboxypeptidase IA is involved in cell wall or envelope synthesis.     

Enzymatic β-galactosidation of β-xylopyranosides

Summary The disaccharides formed by enzymatic transfer of the -D-galactopyranosyl residue fromo-nitrophenyl -d-galactopyranoside to -d-xylopyranosides have been identified. The influence of different factors on the yields of the disaccharides obtained was evaluated. Significant changes in selectivity were observed when -galactosidase fromE. coli was used instead of -galactosidase fromA. oryzae.     

Serine496 of β2 subunit of L-type Ca2+ channel participates in molecular crosstalk between activation of (Na++K+)-ATPase and the channel

Activation of (Na++K+)-ATPase (NKA) regulates cardiac L-type Ca2+ channel (LTCC) function through molecular crosstalk. The mechanism underlying NKA-LTCC crosstalk remains poorly understood. We have previously shown that activation of NKA leads to phosphorylation of LTCC α1 Ser1928. Here we investigated whether LTCC β2 subunit is modulated by NKA activation and found that LTCC β2 Ser496 is phosphorylated in response to activation of NKA. Src inhibitor PP1 and Erk1/2 inhibitor PD98059 abolish LTCC β2 Ser496 phosphorylation, suggesting that NKA-mediated β2 Ser496 phosphorylation is dependent of Src/Erk1/2 signaling pathway. Protein kinase G (PKG) inhibitor KT5823 failed to inhibit the phosphorylation of β2 Ser496, indicating that the NKA-LTCC crosstalk is independent of PKG activity. The results of nifedipine sensitive 45Ca influx experiments suggest that phosphorylation of β2 Ser496 may play a key down-regulation role in attenuating the accelerated activity of α1 subunit of the channel. Ouabain does not cause a phosphorylation on β2 Ser496, indicating a fundamental difference between activation and inhibition of NKA-mediated biological processes. This study provides the first evidence to demonstrate that LTCC β2 subunit is coupled with the movement of signals in the mechanism of activation of NKA-mediated crosstalk with LTCC.     

Expression of the β-subunit of β-conglycinin in seeds of transgenic plants

Soybean (Glycine max (L.) Merr.) seeds contain the storage protein -conglycinin, encoded by a multigene family. -Conglycinin consists of three subunits; , , and . A genomic clone for a -subunit of -conglycinin has been characterized by restriction-enzyme mapping and hybrid selected in-vitro translation followed by immunoprecipitation. In order to determine the developmental regulation of this -subunit gene, its expression was studied in seeds of transgenic petunia (Petunia hybrida) and tobacco (Nicotiana tabacum L.) plants. The -subunit expressed in seeds of petunia and tobacco was recognized by anti--conglycinin serum at a relative molecular mass of 53 000, equivalent to that of the native protein. Separation of the petunia-seed proteins by isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and immunoblot analysis showed that multiple isoelectric forms of the -subunit were produced. There was approximately a twofold variation in the accumulation of the -subunit protein in the mature seeds of transgenic petunia plants, each containing a single -subunit gene. However, the level of protein accumulation in mature seeds and the amount of -subunit mRNA in developing seeds was not correlated. Accumulation of the -subunit protein in transgenic seeds was less than the -subunit protein that accumulated in transgenic petunia seeds containing a single -subunit gene and less than the amount of the -subunit in mature soybean seeds which contain 8–13 -subunit genes. In transgenic tobacco plants, the accumulation of the -subunit protein in seeds was generally well correlated with the number of genes that were incorporated in the different transformants.Abbreviations kb kilobase - kDa kilodalton - M_r relative molecular mass - SDS-PAGE sodium dodecyl sulfate polyacrylamide gel electrophoresis     

Possible Identity of β-Xylosidase and β-Glucosidase of Chaetomium trilaterale

The nature of the active site of Chaetomium trilaterale β-xylosidase catalyzing the hydrolysis of β-d-glucopyranoside and β-d-xylopyranoside was investigated by kinetic methods. On experiments with mixed substrates, such as phenyl β-d-xylopyranoside and phenyl β-d-glucopyranoside, the kinetic features agreed very closely with those features theoretically predicted for a single active site of the same enzyme catalyzing the hydrolysis of these two kinds of substrates.

Both the β-glucosidase and β-xylosidase activities were strongly inhibited by glucono-1,5-lactone and nojirimycin (5-amino-5-deoxy-d-glucopyranose). β-Xylosidase activity was inhibited non-competitively by the two inhibitors, but β-glucosidase activity was competitive. Methyl β-d-xylopyranoside, methyl β-d-glucopyranoside, 1-thiophenyl β-d-xylopyranoside, and 1-thiophenyl β-d-glucopyranoside poorly inhibited both activities. Methyl β-d-xylopyranoside inhibited the β-xylosidase activity competitively but the β-glucosidase activity was non-competitive, whereas methyl β-d-glucopyranoside inhibited the β-xylosidase activity non-competitively but the β-glucosidase activity was competitive. 1-Thiophenyl β-d-xylopyranoside and 1-thiophenyl β-d-glucopyranoside behaved as competitive inhibitors.

From these results, it was concluded that the β-xylosidase and β-glucosidase activities reside in one catalytic site, and this suggests that there might be two kinetically distinct binding sites in the active center of the same enzyme.     

Identification of Novel Peptidyl Serine α-Galactosyltransferase Gene Family in Plants

In plants, serine residues in extensin, a cell wall protein, are glycosylated with O-linked galactose. However, the enzyme that is involved in the galactosylation of serine had not yet been identified. To identify the peptidyl serine O-α-galactosyltransferase (SGT), we chose Chlamydomonas reinhardtii as a model. We established an assay system for SGT activity using C. reinhardtii and Arabidopsis thaliana cell extracts. SGT protein was partially purified from cell extracts of C. reinhardtii and analyzed by tandem mass spectrometry to determine its amino acid sequence. The sequence matched the open reading frame {"type":"entrez-protein","attrs":{"text":"XP_001696927","term_id":"159477661","term_text":"XP_001696927"}}XP_001696927 in the C. reinhardtii proteome database, and a corresponding DNA fragment encoding 748 amino acids ({"type":"entrez-protein","attrs":{"text":"BAL63043","term_id":"377652299","term_text":"BAL63043"}}BAL63043) was cloned from a C. reinhardtii cDNA library. The 748-amino acid protein (CrSGT1) was produced using a yeast expression system, and the SGT activity was examined. Hydroxylation of proline residues adjacent to a serine in acceptor peptides was required for SGT activity. Genes for proteins containing conserved domains were found in various plant genomes, including A. thaliana and Nicotiana tabacum. The AtSGT1 and NtSGT1 proteins also showed SGT activity when expressed in yeast. In addition, knock-out lines of AtSGT1 and knockdown lines of NtSGT1 showed no or reduced SGT activity. The SGT1 sequence, which contains a conserved DXD motif and a C-terminal membrane spanning region, is the first example of a glycosyltransferase with type I membrane protein topology, and it showed no homology with known glycosyltransferases, indicating that SGT1 belongs to a novel glycosyltransferase gene family existing only in the plant kingdom.     

Synthesis of β-Tubanol

Synthesis of β-tubanol (VIa) was achieved by the bromination of dihydro-β-tubanol acetate (VIIb) followed by dehydrobromination and the subsequent hydrolysis. 2,2-Dimethyl-5-hydroxy-chromanone as well as its derivatives (IV) and the corresponding chromanols (V) and chromans (VII) were also prepared.     

Prediction of β-Turns

Kohonen's self-organization model, a neural network model, is applied to predict the β-turns in proteins. There are 455 β-turn tetrapeptides and 3807 non-β-turn tetrapeptides in the training database. The rates of correct prediction for the 110 β-turn tetrapeptides and 30,229 non-β-turn tetrapeptides in the testing database are 81.8% and 90.7%, respectively. The high quality of prediction of neural network model implies that the residue-coupled effect along a polypeptide chain is important for the formation of reversal turns, such as β-turns, during the process of protein folding.     

Negative Role of RIG-I Serine 8 Phosphorylation in the Regulation of Interferon-�� Production

RIG-I (retinoic acid-inducible gene I) and TRIM25 (tripartite motif protein 25) have emerged as key regulatory factors to induce interferon (IFN)-mediated innate immune responses to limit viral replication. Upon recognition of viral RNA, TRIM25 E3 ligase binds the first caspase recruitment domain (CARD) of RIG-I and subsequently induces lysine 172 ubiquitination of the second CARD of RIG-I, which is essential for the interaction with downstream MAVS/IPS-1/CARDIF/VISA and, thereby, IFN-β mRNA production. Although ubiquitination has emerged as a major factor involved in RIG-I activation, the potential contribution of other post-translational modifications, such as phosphorylation, to the regulation of RIG-I activity has not been addressed. Here, we report the identification of serine 8 phosphorylation at the first CARD of RIG-I as a negative regulatory mechanism of RIG-I-mediated IFN-β production. Immunoblot analysis with a phosphospecific antibody showed that RIG-I serine 8 phosphorylation steady-state levels were decreased upon stimulation of cells with IFN-β or virus infection. Substitution of serine 8 in the CARD RIG-I functional domain with phosphomimetic aspartate or glutamate results in decreased TRIM25 binding, RIG-I ubiquitination, MAVS binding, and downstream signaling. Finally, sequence comparison reveals that only primate species carry serine 8, whereas other animal species carry an asparagine, indicating that serine 8 phosphorylation may represent a primate-specific regulation of RIG-I activation. Collectively, these data suggest that the phosphorylation of RIG-I serine 8 operates as a negative switch of RIG-I activation by suppressing TRIM25 interaction, further underscoring the importance of RIG-I and TRIM25 connection in type I IFN signal transduction.     

Serine of β2 subunit of L-type Ca channel participates in molecular crosstalk between activation of (Na+K)-ATPase and the channel

Activation of (Na⁺+K⁺)-ATPase (NKA) regulates cardiac L-type Ca²⁺ channel (LTCC) function through molecular crosstalk. The mechanism underlying NKA-LTCC crosstalk remains poorly understood. We have previously shown that activation of NKA leads to phosphorylation of LTCC α₁ Ser¹⁹²⁸. Here we investigated whether LTCC β₂ subunit is modulated by NKA activation and found that LTCC β₂ Ser⁴⁹⁶ is phosphorylated in response to activation of NKA. Src inhibitor PP1 and Erk1/2 inhibitor PD98059 abolish LTCC β₂ Ser⁴⁹⁶ phosphorylation, suggesting that NKA-mediated β₂ Ser⁴⁹⁶ phosphorylation is dependent of Src/Erk1/2 signaling pathway. Protein kinase G (PKG) inhibitor KT5823 failed to inhibit the phosphorylation of β₂ Ser⁴⁹⁶, indicating that the NKA-LTCC crosstalk is independent of PKG activity. The results of nifedipine sensitive ⁴⁵Ca influx experiments suggest that phosphorylation of β₂ Ser⁴⁹⁶ may play a key down-regulation role in attenuating the accelerated activity of α₁ subunit of the channel. Ouabain does not cause a phosphorylation on β₂ Ser⁴⁹⁶, indicating a fundamental difference between activation and inhibition of NKA-mediated biological processes. This study provides the first evidence to demonstrate that LTCC β₂ subunit is coupled with the movement of signals in the mechanism of activation of NKA-mediated crosstalk with LTCC.     

Folding of β-Hairpins

Identification of the factors governing the formation of -structure independently of the rest of the protein is important for understanding the folding process of protein into a unique native structure. It has been shown that some -hairpins can fold autonomously into native-like structures, either in aqueous solution or in the presence of an organic co-solvent. Our aim is to review recent theoretical and experimental studies of folding of -structures.     

Prediction of β-Turns

Kohonen's self-organization model, a neural network model, is applied to predict the -turns in proteins. There are 455 -turn tetrapeptides and 3807 non--turn tetrapeptides in the training database. The rates of correct prediction for the 110 -turn tetrapeptides and 30,229 non--turn tetrapeptides in the testing database are 81.8% and 90.7%, respectively. The high quality of prediction of neural network model implies that the residue-coupled effect along a polypeptide chain is important for the formation of reversal turns, such as -turns, during the process of protein folding.     

Selenium-mediated differential response of β-glucosidase and β-galactosidase of germinatingTrigonella foenum-graecum

β-Glucosidase and β-galactosidase activity profile tested in different seeds during 24 h germination revealed reasonably high levels of activity inVigna radiata, Cicer arietinum, andTrigonella foenum-graecum. In all seeds tested, β-galactosidase activity was, in general, higher than that of β-glucosidase.T. foenum-graecum seedlings exhibited maximal total and specific activities for both the enzymes during 72 h germination. Se supplementation as Na₂SeO₃ up to 0.75 ppm was found to be beneficial to growth and revealed selective enhancement of β-galactosidase activity by 40% at 0.5 ppm Se. The activities of both the enzymes drastically decreased at 1.0 ppm level of Se supplementation. On the contrary, addition of Na₂SeO₃ in vitro up to 1 ppm to the enzyme extracts did not influence these activities. Hydrolytic rates of β-glucosidase in both control and Se-supplemented groups were enhanced by 20% with 0.05M glycerol in the medium and 30% at 0.1M glycerol. The rates were marginally higher in Se-supplemented seedlings than the controls, irrespective of added glycerol in the medium. In contrast, hydrolysis by β-galactosidase showed a trend of decrease in Se-supplemented seedlings compared to the control, when glycerol was present in the medium. Addition of Se in vitro in the assay medium showed no difference in the hydrolytic rate by β-galactosidase when compared to control, while the activity of β-glucosidase declined by 50%. Se-grown seedlings showed an enhancement of transglucosidation rate by 40% in the presence of 0.1M glycerol. The study reveals a differential response to Se among the β-galactosidase and β-glucosidase ofT. foenumgraecum with increase in the levels of β-galactosidase activity.     

Hydrolysis of β-Galactosyl Ester Linkage by β-Galactosidases

p-Hydroxybenzoyl β-galactose (pHB-Gal) was synthesized chemically to examine the hydrolytic activity of β-galactosyl ester linkage by β-galactosidases. The enzyme from Penicillium multicolor hydrolyzed the substrate as fast as p-nitrophenyl β-galactoside (pNP-Gal), a usual substrate with a β-galactosidic linkage. The enzymes from Escherichia coli and Aspergillus oryzae hydrolyzed pHB-Gal with almost the same rates as pNP-Gal. The enzymes from Bacillus circulans, Saccharomyces fragilis, and bovine liver showed much lower activities. pH-activity profiles, inhibition analysis, and kinetic properties of the enzymic reaction on pHB-Gal suggested that β-galactosidase had only one active site for hydrolysis of both galactosyl ester and galactoside. The Penicillium enzyme hydrolyzed pHB-Gal in the presence of H₂ ¹⁸O to liberate galactose containing ¹⁸O. This result suggests the degradation occurs between the anomeric carbon and an adjacent O atom in the ester linkage of pHB-Gal.     

Preparation of Aryl β-d-Mannopyranoside Derivatives via β-d-arabino-Hexopyranosiduloses

Sequential oxidation and reduction of aryl 4, 6-O-benzylidene-β-d-glucosides with dimethyl sulfoxide-phosphorus pentoxide mixture (DMSO–P₂O₅) and sodium borohydride were carried out as a new means for the preparation of aryl β-d-mannopyranoside derivatives. p-Nitrophenyl 4, 6-O-benzylidene-β-d-mannopyranoside was obtained in 22% yield from the corresponding glucoside 3-O-acetate, whereas from the unprotected acetal, 4, 6-O-benzylidene acetals of the corresponding mannoside and alloside were isolated in the yields of 6.7 and 2.1%, respectively. Similarly, phenyl 4, 6-O-benzylidene β-d-mannoside, alloside, and altroside were obtained from the corresponding glucoside in 2.2, 0.8 and 2.1% yields, respectively.     

Synthesis of derivatives of methyl β-sophoroside

Selective tritylation of methyl β-sophoroside (1) and subsequent acetylation gave the 3,4,2′,3′,4′-penta-O-acetyl-6,6′-di-O-trityl derivative, which was O-detritylated, and the product p-toluenesulfonylated, to give methyl 3,4,2′,3′,4′-penta-O-acetyl-6,6′-di-O-p-tolylsulfonyl-β-sophoroside (4) in 63% net yield. Compound 4 was also obtained in 69% yield by p-toluenesulfonylation of 1, followed by acetylation. Several, 6,6′-disubstituted derivatives of 1 were synthesized by displacement reactions of 4 with various nucleophiles. Treatment of 4 with sodium methoxide afforded methyl 3,6:3′,6′-dianhydro-β-sophoroside. Several 6- and 6′-monosubstituted derivatives of 1 were prepared, starting from the 4,6-O-benzylidene derivative of 1.