2-Keto-3-Deoxygluconate 6-Phosphate Aldolase Mutants of Escherichia coli

A new mutation in Escherichia coli, giving inability to grow on gluconic, glucuronic, or galacturonic acids, has been identified as complete deficiency of 2-keto-3-deoxygluconate 6-phosphate (KDGP) aldolase activity. The genetic map position of the locus, eda, is about 35 min. The inability to grow on the uronic acids was expected, because the aldolase is on the sole known pathway of their metabolism. However, inability to grow on gluconate was less expected, because the hexose monophosphate shunt might be used, as happens in mutants blocked in the previous step, edd, of the Entner-Doudoroff pathway. The likely explanation of gluconate negativity is inhibition by accumulated KDGP, because gluconate is inhibitory to growth on other substances, and one type of gluconate revertant is eda(-), edd(-). KDGP is probably the inducer of KDGP aldolase.     

Variable Sugar Fermentation by Clostridia

Forty-two sugar fermentation characteristics recorded as “d” in the 8th edition of Bergey's Manual of Determinative Bacteriology were reinvestigated by using eight different peptone media and 205 strains of nine species of pathogenic Clostridia. In the absence of sugar, the final pH of 7-day cultures in the basal medium varied widely depending on the peptone employed, the species tested, and even the strain of the species. In the presence of sugar, the final pH of 7-day cultures was markedly influenced by these factors. Since the sugars with reactions recorded as “d” were weakly fermented and, consequently, the fermentation reactions were easily affected by cultural variations resulting in strain instability, we employed the pH difference method (ΔpH method) in which the pH difference of 0.5 between cultures with and without sugar was used as the critical level. Thirty-six (86%) of the 42 sugar reactions recorded as “d” were sorted into “+” or “-” by the ΔpH method. Six sugars, however, still remained as “d” because of their extremely weak fermentation characters. The use of the ΔpH method in any peptone medium not only minimizes incorrect evaluation but also can provide some distinct criteria for identification of Clostridia.     

Formate as an Intermediate in the Bovine Rumen Fermentation

An average of 11 (range, 2 to 47) mumoles of formate per g per hr was produced and used in whole bovine rumen contents incubated in vitro, as calculated from the product of the specific turnover rate constant, k, times the concentration of intercellular formate. The latter varied between 5 and 26 (average, 12) nmoles/g. The concentration of formate in the total rumen contents was as much as 1,000 times greater, presumably owing to formate within the microbial cells. The concentration of formate in rumen contents minus most of the plant solids was varied, and from the rates of methanogenesis the Michaelis constant, K(m), for formate conversion to CH(4) was estimated at 30 nmoles/g. Also, the dissolved H(2) was measured in relation to methane production, and a K(m) of 1 nmole/g was obtained. A pure culture of Methanobacterium ruminantium showed a K(m) of 1 nmole of H(2)/g, but the K(m) for formate was much higher than the 30 nmoles for the rumen contents. It is concluded that nonmethanogenic microbes metabolize intercellular formate in the rumen. CO(2) and H(2) are the principal substrates for rumen methanogenesis. Eighteen per cent of the rumen methane is derived from formate, as calculated from the intercellular concentration of hydrogen and formate in the rumen, the Michaelis constants for conversion of these substrates by rumen liquid, and the relative capacities of whole rumen contents to ferment these substrates.     

葡萄糖酸钠的发酵及其抑菌实验

利用黑曲霉发酵法生产葡萄糖酸钠,通过参数检测研究各参数及黑曲霉生理活性的变化规律。通过正交试验优化发酵,最终确定发酵参数为：16.5 h种龄、15%转种量和pH 5.8。验证葡萄糖酸钠抑菌效果,最终确定饲料中可添加量为0.5%~0.7%,为葡萄糖酸钠在饲料行业中的应用提供理论依据。     

葡萄糖酸钙对L-组氨酸发酵的影响及条件优化

目的：提高L-组氨酸的产量并且得出最佳发酵条件。方法：在L-组氨酸的摇瓶发酵实验中,加入20g/L的葡萄糖酸钙,对发酵条件进行优化。结果：L-组氨酸的产量大幅度提高,产酸量由3.00g/L提高到7.50g/L。条件优化后L-组氨酸的产量提高到9.30g/L。结论：发酵培养基中20g/L的葡萄糖酸钙的加入能够诱导葡萄糖酸激酶生成,大幅度提高其比活,增大磷酸戊糖（HMP）途径的通量。有利于L-组氨酸的合成、菌体的生长。     

Formation of 3-Keto-4-deoxypentosone and 3-Hydroxy-2-pyrone by the Degradation of Dehydro-l-ascorbic Acid

A crystalline phenylhydrazone was obtained when a heated solution of dehydro-l-ascorbic acid (DHA) was treated with phenylhydrazine-HCl. Its molecular formula was C₁₇H₁₈N₄O₂, and the structure was determined to be 1,2-bis(phenylhydrazone) of 3-keto-4-deoxypentosone, a new tricarbonyl compound which was considered to be one of the possible intermediates of the browning reaction of DHA. 3-Hydroxy-2-pyrone was also isolated from the ether extract of the heated DHA solution as a main aroma compound produced from DHA. Possible formation mechanisms of these compounds were discussed.     

葡萄糖酸钠发酵过程中对pH细化控制的研究

在黑曲霉发酵生产葡萄糖酸钠的过程中,通过在不同发酵阶段控制不同的pH,可缩短生产周期,提高生产效率。比较5 L发酵罐中控制pH 5.0、pH 5.2、pH 5.4、pH 5.6条件下葡萄糖酸钠发酵情况,通过在线检测系统和离线数据分析,考察不同pH对降糖速率和葡萄糖氧化酶活性的影响,确定发酵前期pH控制在5.6,后期pH控制在5.2。     

2-Keto-3-fluoroglutarate: a useful mechanistic probe of 2-keto-glutarate-dependent enzyme systems

2-Keto-3-fluoroglutaric acid prepared by acid hydrolysis of its diethyl ester is stable, as the free acid in aqueous solution at pH 2, and can be stored at -20 degrees C for several years. Both enantiomers are reduced by NADH in the presence of glutamate dehydrogenase (EC 1.4.1.2) to the two diastereomers of 3-fluoro-L-glutamate, which are stable at neutral pH and at high pH unless heated. 2-Keto-3-fluoroglutarate exists in solution almost entirely as a hydrate both at low and neutral pH. Both enantiomers of ketofluoroglutarate react with the pyridoxamine forms of aspartate, alanine and 4-aminobutyrate transaminases to give fluoride release. 2 mol of cosubstrate amino acid react for each mol of ketofluoroglutarate (KFG) when starting from the pyridoxamine form of the enzyme: 2 RCHNH2COOH + KFG + H2O----F- + NH4+ + glutamate + 2 RCOCOOH. Both diastereomers of fluoroglutamate are decarboxylated by glutamate decarboxylase (EC 4.1.1.15) with fluoride release: KFG + H2O----CO2 + F- + HCOCH2CH2COOH. By contrast, only one isomer of fluoroglutamate will react with the pyridoxal form of glutamate-oxalacetate transaminase to give fluoride release: HOOCCHNH2CHFCH2COOH + H2O----4F- + NH4+ + HOOCCOCH2CH2COOH. The enzymatic decarboxylation of 3-fluoroisocitrate produces only one enantiomer of ketofluoroglutarate, which is reduced to threo (2R,3R)-3-fluoroglutamate by NADH and glutamate dehydrogenase: [2R,3S]-HOOCCH(OH)CF(COOH)CH2COOH + NADP+----[3R]-KFG + CO2 + NADPH + H+. The proton, 13C, and 19F-NMR parameters of ketofluoroglutarate and the two fluoroglutamate diastereomers are presented. These molecules are useful probes of enzymatic mechanisms thought to involve carbanion intermediates.     

2-Keto-4-methylthiobutyrate, an intermediate in the methionine salvage pathway, is a good substrate for CtBP1

In the present work, we have studied the kinetic properties of the catalytic domain of CtBP1, a co-repressor belonging to the d-2-hydroxyacid dehydrogenase family and known to reduce pyruvate in the presence of NADH. CtBP1 acted on a variety of alpha-keto acids, for which it displayed biphasic curves with inhibition at elevated concentrations, as observed with other dehydrogenases of the same family. Based on catalytic efficiencies, the best substrate was 2-keto-4-methylthiobutyrate, an intermediate of the methionine salvage pathway. It was about 20-fold better than 2-ketoisocaproate and glyoxylate, and 80-fold better than pyruvate. From these data we conclude that 2-keto-4-methylthiobutyrate may be an important regulator of CtBP activity, possibly linking gene repression to the activity of the methionine salvage and spermine synthesis pathways.     

Structure of Thermus thermophilus 2-Keto-3-deoxygluconate kinase: evidence for recognition of an open chain substrate

2-Keto-3-deoxygluconate kinase (KDGK) catalyzes the phosphorylation of 2-keto-3-deoxygluconate (KDG) to 2-keto-3-deoxy-6-phosphogluconate (KDGP). The genome sequence of Thermus thermophilus HB8 contains an open reading frame that has a 30% identity to Escherichia coli KDGK. The KDGK activity of T.thermophilus protein (TtKDGK) has been confirmed, and its crystal structure has been determined by the molecular replacement method and refined with two crystal forms to 2.3 angstroms and 3.2 angstroms, respectively. The enzyme is a hexamer organized as a trimer of dimers. Each subunit is composed of two domains, a larger alpha/beta domain and a smaller beta-sheet domain, similar to that of ribokinase and adenosine kinase, members of the PfkB family of carbohydrate kinases. Furthermore, the TtKDGK structure with its KDG and ATP analogue was determined and refined at 2.1 angstroms. The bound KDG was observed predominantly as an open chain structure. The positioning of ligands and the conservation of important catalytic residues suggest that the reaction mechanism is likely to be similar to that of other members of the PfkB family, including ribokinase. In particular, the Asp251 is postulated to have a role in transferring the gamma-phosphate of ATP to the 5'-hydroxyl group of KDG.     

Interaction of the chiral pyruvate analog, 2-keto-3-bromobutyrate, with pyruvate lyases. 2-Keto-3-deoxygluconate-6-phosphate aldolase of Pseudomonas putida.

The enzyme 2-keto-3-deoxygluconate-6-P aldolase of Pseudomonas putida is inactivated by one of the chiral forms of 2-keto-(3RS)-3-bromobutyric acid (bromoketobutyrate). The inactivation shows saturation kinetics and competition with pyruvate. The minimal inactivation half-time is 4 min and that concentration of bromoketobutyrate half-saturating the enzyme is 2 mM. (3RS)-[3-3H]bromoketobutyrate is catalytically detritiated during enzyme inactivation. A kinetic analysis of rates gave data consistent with both catalysis and inactivation occurring at a single protein site, the catalytic site. The enzyme only detritiates one of the two optical isomers of bromoketobutyrate, and that form which is detritiated also alkylates the catalytic site. The inactive isomer of reagent degrades, with inversion, to L-lactate so that the chiral form specific for the enzyme is 2-keto-(3S)-3-bromobutyrate. Thus, as is the case with bromopyruvate, the enzyme catalyzes protonation of the re face at C-3 of the enzyme-reagent eneamine. As a result, bromoketobutyrate could serve as a chiral probe for stereochemical constraints of selected pyruvate-specific lyase active sites.     

Genetic Control of the 2-Keto-3-Deoxy-d-Gluconate Metabolism in Escherichia coli K-12: kdg Regulon

2-Keto-3-deoxy-gluconate (KDG), an intermediate of the hexuronate pathway in Escherichia coli K-12, is utilized as the sole carbon source only in strains derepressed for the specific KDG-uptake system. KDG is metabolized to pyruvate and glyceraldehyde-3-phosphate via the inducible enzymes KDG-kinase and 2-keto-3-deoxy-6-phosphate-gluconate (KDPG) aldolase. However, another inducible pathway, where the KDG is the branch point, has been demonstrated. Genetic studies of the KDG degradative pathway reported in this paper led to the location of KDG kinase-negative and pleiotropic constitutive mutations. The kdgK locus, presumably the structural gene of the kinase, occurs at min 69 and is co-transducible with xyl. The mutants, simultaneously constitutive for the uptake, kinase, and aldolase, define a kdgR locus at min 36 between the co-transducible markers kdgA and oldD. As to the nature of the control exerted by the kdgR product, we have shown the following. (i) Thermosensitive mutants of the kdgR locus are inducible at low temperature but derepressed at 42 C for the three operons—kdgT (transport system), kdgK, and kdgA (KDPG aldolase). (ii) The kdgR⁺ allele is dominant to the kdgR constitutive allele. (iii) A deletion in kdgA extending into the regulatory gene, kdgR, leads to a constitutive expression of the nondeleted operons—kdgT and kdgK. These properties demonstrate that the kdg regulon is negatively controlled by the kdgR product. It is presumed that differences in operator and in promotor structures could explain the strong decoordination, respectively, in the induction and catabolic repression, of these three enzymes activities.     

Production of Hydrocinnamic Acid by Clostridia

Hydrocinnamic acid was found in acid extracts of spent growth medium from cultures of Clostridium sporogenes. The acid was identified by mass spectrometry and its identity was confirmed by gas chromatography. The acid was produced in relatively large amounts (2 to 3 μmoles/ml of medium) by C. sporogenes, toxigenic types A, B, D, and F of C. botulinum, and some strains of C. bifermentans. Other strains of C. bifermentans and strains of C. sordellii and C. caproicum produced only small amounts (0.1 to 0.4 μmoles/ml) of the acid. The acid was not detected in spent medium from toxigenic types C and E of C. botulinum or from 25 other strains representing eight Clostridium species. Resting cell suspensions exposed to l-phenylalanine produced hydrocinnamic and cinnamic acid; the latter compound probably functions as an intermediate in the metabolism of l-phenylalanine.     

Methoxyhydroquinone, an Intermediate of Vanillate Catabolism by Polyporus dichrous

Vanillate was metabolized by Polyporus dichrous in liquid culture via methoxyhydroquinone. Protocatechuate, gentisate, and hydroquinone were not affected by vanillate-metabolizing mycelial pellets that readily degraded methoxyhydroquinone.     

脱氨神经氨酸及其在肿瘤中表达的研究进展

脱氨神经氨酸(2-keto-3-deoxy-D-glycero-D-galacto-nononic acid,KDN)是唾液酸家族中的三种核心成员之一。KDN单体主要由甘露糖作为前体糖合成得到,KDN大量存在于低等脊椎动物和细菌中,而在哺乳动物中的表达量却很低。近期,有研究报道,KDN在人类肿瘤中高表达,并且会随着肿瘤恶性程度的增高呈正相关增长,因此,推测KDN可能是某些肿瘤的肿瘤标示物。本文介绍了KDN的结构及其生物合成,重点综述了KDN在生物体内及肿瘤中的表达等研究现状,为以后深入研究KDN奠定了良好的基础。     

Properties of 2-C-Methyl-D-Erythritol 2,4-Cyclopyrophosphate,an Intermediate in Nonmevalonate Isoprenoid Biosynthesis

Extraction and purification from the biomass of Corynebacterium ammoniagenes of 2-C-methyl-D-erythritol 2,4-cyclopyrophosphate (MEC) was associated with its spontaneous transformation into a number of derivatives (which was due to the pyrophosphate bond lability and the formation of complexes with metals). These derivatives included 1,2-cyclophospho-4-phosphate, 2,4-diphosphate, 2,3-cyclophosphate, 1,4-diphosphate, and 3,5-diphosphate (identified by ¹H, ³¹P, and ¹³C NMR spectroscopy) and accounted for about 10% of the MEC. When added to a solution of DNA in the presence of the Fenton reagent, MEC prevented DNA decomposition. In addition, MEC slowed down the interaction of the reagent with tempol radicals, which indicates that complexation of ferrous ions by MEC attenuates their ability to catalyze the formation of hydroxyl radicals from hydrogen peroxide. In the presence of 0.23 mM MEC, the rate of respiration of rat liver mitochondria increased by 1.8 times. At 0.1–1.0 mM, MEC activated in vitro proliferation of human Vgamma9 T cells. It is suggested that MEC acts as an endogenous stabilizing agent for bacterial cells subjected to oxidative stress and as an immunomodulator for eukaryotic hosts.     

3-Keto-5-aminohexanoate cleavage enzyme: a common fold for an uncommon Claisen-type condensation

The exponential increase in genome sequencing output has led to the accumulation of thousands of predicted genes lacking a proper functional annotation. Among this mass of hypothetical proteins, enzymes catalyzing new reactions or using novel ways to catalyze already known reactions might still wait to be identified. Here, we provide a structural and biochemical characterization of the 3-keto-5-aminohexanoate cleavage enzyme (Kce), an enzymatic activity long known as being involved in the anaerobic fermentation of lysine but whose catalytic mechanism has remained elusive so far. Although the enzyme shows the ubiquitous triose phosphate isomerase (TIM) barrel fold and a Zn(2+) cation reminiscent of metal-dependent class II aldolases, our results based on a combination of x-ray snapshots and molecular modeling point to an unprecedented mechanism that proceeds through deprotonation of the 3-keto-5-aminohexanoate substrate, nucleophilic addition onto an incoming acetyl-CoA, intramolecular transfer of the CoA moiety, and final retro-Claisen reaction leading to acetoacetate and 3-aminobutyryl-CoA. This model also accounts for earlier observations showing the origin of carbon atoms in the products, as well as the absence of detection of any covalent acyl-enzyme intermediate. Kce is the first representative of a large family of prokaryotic hypothetical proteins, currently annotated as the "domain of unknown function" DUF849.