Purification and Characterization of l-Leucine-α-ketoglutarate Transaminase from Acetobader suboxydans

l-Leucine-α-ketoglutarate (α-KGA) transaminase from Acetobacter suboxydans was purified to the state of homogeneity by the criteria of ultracentrifugation and electrophoresis on a cellulose acetate membrane. The molecular weight was about 80,000 and one mole of pyridoxal 5′-phosphate was bound per mole of enzyme as a coenzyme. The enzyme exhibited absorption maxima at 280, 337 and 414 nm.

The branched-chain amino acids and α-KGA were specific as amino donors and an acceptor. l-Leucine-α-KGA transaminase is suggested to correspond to the enzyme so-called Transaminase B.     

Distribution and Properties of NAD Phosphorylating Reaction

Distribution of NAD phosphorylating reactions, phosphorylation through NAD kinase and phosphotransferase, was investigated. NAD kinase activity was distributed rather widely in bacteria, whereas phosphotransferase activity with p-NPP and NAD was limited to a few genera. Proteus mirabilis showed strong activity of phosphotransferase besides NAD kinase activity.

Partial purification of the phosphotransferase was attempted. The enzyme preparation possessed phosphatase activity as well as phosphotransferase activity. Phosphorylation of NAD proceeded maximally under the conditions below pH 4.0. Cu²⁺ showed stimulating effect on the activity. Besides p-NPP and phenylphosphate, various nucleotides, especially 2′ (or 3′) isomers, served as excellent phosphoryl donors, and various kinds of nucleosides and nucleotides were phosphorylated to form nucleoside monophosphates and nucleoside diphosphates.     

A web services choreography scenario for interoperating bioinformatics applications

Background  

Very often genome-wide data analysis requires the interoperation of multiple databases and analytic tools. A large number of genome databases and bioinformatics applications are available through the web, but it is difficult to automate interoperation because: 1) the platforms on which the applications run are heterogeneous, 2) their web interface is not machine-friendly, 3) they use a non-standard format for data input and output, 4) they do not exploit standards to define application interface and message exchange, and 5) existing protocols for remote messaging are often not firewall-friendly. To overcome these issues, web services have emerged as a standard XML-based model for message exchange between heterogeneous applications. Web services engines have been developed to manage the configuration and execution of a web services workflow.     

DNA binding and protein-protein interaction sites in MutS, a mismatched DNA recognition protein from Thermus thermophilus HB8

The mismatch repair system repairs mismatched base pairs, which are caused by either DNA replication errors, DNA damage, or genetic recombination. Mismatch repair begins with the recognition of mismatched base pairs in DNA by MutS. Protein denaturation and limited proteolysis experiments suggest that Thermus thermophilus MutS can be divided into three structural domains as follows: A (N-terminal domain), B (central domain), and C (C-terminal domain) (Tachiki, H., Kato, R., Masui, R., Hasegawa, K., Itakura, H., Fukuyama, K., and Kuramitsu, S. (1998) Nucleic Acids Res. 26, 4153-4159). To investigate the functions of each domain in detail, truncated genes corresponding to the domains were designed. The gene products were overproduced in Escherichia coli, purified, and assayed for various activities. The MutS-MutS protein interaction site was determined by size-exclusion chromatography to be located in the B domain. The B domain was also found to possess nonspecific double-stranded DNA-binding ability. The C domain, which contains a Walker's A-type nucleotide-binding motif, demonstrated ATPase activity and specific DNA recognition of mismatched base pairs. These ATPase and specific DNA binding activities were found to be dependent upon C domain dimerization.     

Characteristics and Efficiency of Glutamine Production by Coupling of a Bacterial Glutamine Synthetase Reaction with the Alcoholic Fermentation System of Baker’s Yeast

Glutamine production with bacterial glutamine synthetase (GS) and the sugar-fermenting system of baker’s yeast for ATP regeneration was investigated by determining the product yield obtained with the energy source for ATP regeneration (i.e., glucose) for yeast fermentation. Fructose 1,6-bisphosphate was accumulated temporarily prior to the formation of glutamine in mixtures which consisted of dried yeast cells, GS, their substrate (glucose and glutamate and ammonia), inorganic phosphate, and cofactors. By an increase in the amounts of GS and inorganic phosphate, the amounts of glutamine formed increased to 19 to 54 g/liter, with a yield increase of 69 to 72% based on the energy source (glucose) for ATP regeneration. The analyses of sugar fermentation of the yeast in the glutamine-producing mixtures suggested that the apparent hydrolysis of ATP by a futile cycle(s) at the early stage of glycolysis in the yeast cells reduces the efficiency of ATP utilization. Inorganic phosphate inhibits phosphatase(s) and thus improves glutamine yield. However, the analyses of GS activity in the glutamine-producing mixtures suggested that the higher concentration of inorganic phosphate as well as the limited amount of ATP-ADP caused the low reactivity of GS in the glutamine-producing mixtures. A result suggestive of improved glutamine yield under the conditions with lower concentrations of inorganic phosphate was obtained by using a yeast mutant strain that had low assimilating ability for glycerol and ethanol. In the mutant, the activity of the enzymes involved in gluconeogenesis, especially fructose 1,6-bisphosphatase, was lower than that in the wild-type strain.     

Characteristics and Efficiency of Glutamine Production by Coupling of a Bacterial Glutamine Synthetase Reaction with the Alcoholic Fermentation System of Baker’s Yeast

Glutamine production with bacterial glutamine synthetase (GS) and the sugar-fermenting system of baker’s yeast for ATP regeneration was investigated by determining the product yield obtained with the energy source for ATP regeneration (i.e., glucose) for yeast fermentation. Fructose 1,6-bisphosphate was accumulated temporarily prior to the formation of glutamine in mixtures which consisted of dried yeast cells, GS, their substrate (glucose and glutamate and ammonia), inorganic phosphate, and cofactors. By an increase in the amounts of GS and inorganic phosphate, the amounts of glutamine formed increased to 19 to 54 g/liter, with a yield increase of 69 to 72% based on the energy source (glucose) for ATP regeneration. The analyses of sugar fermentation of the yeast in the glutamine-producing mixtures suggested that the apparent hydrolysis of ATP by a futile cycle(s) at the early stage of glycolysis in the yeast cells reduces the efficiency of ATP utilization. Inorganic phosphate inhibits phosphatase(s) and thus improves glutamine yield. However, the analyses of GS activity in the glutamine-producing mixtures suggested that the higher concentration of inorganic phosphate as well as the limited amount of ATP-ADP caused the low reactivity of GS in the glutamine-producing mixtures. A result suggestive of improved glutamine yield under the conditions with lower concentrations of inorganic phosphate was obtained by using a yeast mutant strain that had low assimilating ability for glycerol and ethanol. In the mutant, the activity of the enzymes involved in gluconeogenesis, especially fructose 1,6-bisphosphatase, was lower than that in the wild-type strain.Glutamine is one of the most important compounds in nitrogen metabolism; it is not only a constituent of proteins but is also a donor of the amino (amido) moiety in the biosynthesis of other amino acids, purines, pyrimidines, pyridine coenzymes, and complex carbohydrates. Glutamine is also used in the treatment of gastric ulcers and has been produced commercially by direct fermentation with certain bacteria (6–10).In recent years, enzymatic synthesis has come to rival direct fermentation as a means of producing amino acids. In the case of glutamine, however, the need for a stoichiometric supply of ATP for the endoergonic reaction of glutamine synthetase (GS) precludes the development of an economically valuable method, unless ATP can be regenerated and recycled.Processes for the production of various substances using dried yeast cells as an enzyme source were established by Tochikura and colleagues (2, 4, 16, 18–20). The processes are driven by the chemical energy of ATP released by the alcoholic fermentation by the yeast, which has been wasted in alcoholic brewing (17). Tochikura and colleagues also designed a process in which the yeast fermentation of sugar is combined with an endoergonic reaction catalyzed by an enzyme from a different microorganism (3). The results suggest that the process offers the possibility of producing many compounds at a high yield by using various biosynthetic reactions and high concentrations of substrates. Tochikura et al. introduced the general idea of coupled fermentation with energy transfer for the process; its principle is indicated in Fig. ​Fig.1,1, with glutamine production as an example. Open in a separate windowFIG. 1Scheme of glutamine production by the coupled fermentation with energy transfer method. ∗1, glycolytic pathway is abridged. ∗2, inorganic phosphate (P_i) is recycled.In the process of coupled fermentation with energy transfer, a catalytic amount of ATP is regenerated with the energy of sugar fermented by yeast, in the form of baker’s yeast (4, 16, 18, 19, 23). The energy-utilizing system for the synthesis can involve the enzyme(s) of yeast itself or those of other organisms. It should be noted that, from another point of view, the use of the energy-utilizing system results in ADP regeneration to complete the fermentation of glucose, and that, if there is no ADP regeneration, the yeast fermentation of sugar can proceed only as follows, in the presence of inorganic phosphate (the Harden-Young effect of inorganic phosphate [1]), 2 · glucose + 2 · inorganic phosphate → fructose 1,6-bisphosphate (FBP) + 2 · C₂H₅OH + 2 · CO₂ (Harden-Young equation), where ADP regeneration for the fermentation of 1 mol of glucose is carried out by the phosphorylation of another mole of glucose to FBP.We previously reported glutamine production, obtained by employing a combination of baker’s yeast cells and GS from Gluconobacter suboxydans, as the first application of the coupled fermentation with energy transfer method for the production of a nonphosphorylated compound (12, 13). In addition, we achieved high-yield glutamine production by using the Corynebacterium glutamicum (Micrococcus glutamicus) enzyme and larger amounts of the substrates (15). The maximum amounts of glutamine formed (23 to 25 g/liter) and the yield based on glutamate (50 to 100%) were to some extent satisfactory, but the yield based on the energy source (glucose) for ATP regeneration was not satisfactory (about 40% of the theoretical value; 2 mol of glutamine can be formed when 1 mol of glucose is consumed).In the present study, we examined the characteristics of glutamine production regarding product yield based on the energy source for ATP regeneration and regarding the reactivity of GS during glutamine production, which is closely related to the product yield. The results of preliminary attempts to improve glutamine production are also described. In these experiments, a yeast mutant which has a low assimilating ability for glycerol and/or ethanol was used.     

N-terminal region of chitinase I of Bacillus circulans KA-304 contained new chitin-biding domain

Chitinase I (CHI1) of Bacillus circulans KA-304 forms protoplasts from Schizophyllum commune mycelia when the enzyme is combined with α-1,3-glucanase of B. circulans KA-304. CHI1 consists of an N-terminal unknown region and a C-terminal catalytic region classified into the glycoside hydrolase family-19 type. An N-terminal region-truncated mutant of CHI 1 (CatCHI1), which was expressed in Escherichia coli Rosetta-gami B (DE3), lost colloidal chitin- and powder chitin-binding activities. The colloidal chitin- and the powder chitin-hydrolyzing activities of CatCHI1 were lower than those of CHI1, and CatCHI1 was not effective in forming the protoplast. A fusion protein of the N-terminal region of CHI1 and green fluorescent protein (Nterm-GFP) was expressed in E. coli, and the fusion protein was adsorbed to colloidal chitin, powder chitin, and chitosan. Fluorescence microscopy analysis showed that Nterm-GFP bound to the S. commune cell-wall.     

Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis

Introduction  

The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis.     

Characterization of salt-tolerant glutaminase from Stenotrophomonas maltophilia NYW-81 and its application in Japanese soy sauce fermentation

Glutaminase from Stenotrophomonas maltophilia NYW-81 was purified to homogeneity with a final specific activity of 325 U/mg. The molecular mass of the native enzyme was estimated to be 41 kDa by gel filtration. A subunit molecular mass of 36 kDa was measured with SDS-PAGE, thus indicating that the native enzyme is a monomer. The N-terminal amino acid sequence of the enzyme was determined to be KEAETQQKLANVVILATGGTIA. Besides l-glutamine, which was hydrolyzed with the highest specific activity (100%), l-asparagine (74%), d-glutamine (75%), and d-asparagine (67%) were also hydrolyzed. The pH and temperature optima were 9.0 and approximately 60°C, respectively. The enzyme was most stable at pH 8.0 and was highly stable (relative activities from 60 to 80%) over a wide pH range (5.0–10.0). About 70 and 50% of enzyme activity was retained even after treatment at 60 and 70°C, respectively, for 10 min. The enzyme showed high activity (86% of the original activity) in the presence of 16% NaCl. These results indicate that this enzyme has a higher salt tolerance and thermal stability than bacterial glutaminases that have been reported so far. In a model reaction of Japanese soy sauce fermentation, glutaminase from S. maltophilia exhibited high ability in the production of glutamic acid compared with glutaminases from Aspergillus oryzae, Escherichia coli, Pseudomonas citronellolis, and Micrococcus luteus, indicating that this enzyme is suitable for application in Japanese soy sauce fermentation.