Metabolic Engineering of a Novel Muconic Acid Biosynthesis Pathway via 4-Hydroxybenzoic Acid in Escherichia coli

cis,cis-Muconic acid (MA) is a commercially important raw material used in pharmaceuticals, functional resins, and agrochemicals. MA is also a potential platform chemical for the production of adipic acid (AA), terephthalic acid, caprolactam, and 1,6-hexanediol. A strain of Escherichia coli K-12, BW25113, was genetically modified, and a novel nonnative metabolic pathway was introduced for the synthesis of MA from glucose. The proposed pathway converted chorismate from the aromatic amino acid pathway to MA via 4-hydroxybenzoic acid (PHB). Three nonnative genes, pobA, aroY, and catA, coding for 4-hydroxybenzoate hydrolyase, protocatechuate decarboxylase, and catechol 1,2-dioxygenase, respectively, were functionally expressed in E. coli to establish the MA biosynthetic pathway. E. coli native genes ubiC, aroF^FBR, aroE, and aroL were overexpressed and the genes ptsH, ptsI, crr, and pykF were deleted from the E. coli genome in order to increase the precursors of the proposed MA pathway. The final engineered E. coli strain produced nearly 170 mg/liter of MA from simple carbon sources in shake flask experiments. The proposed pathway was proved to be functionally active, and the strategy can be used for future metabolic engineering efforts for production of MA from renewable sugars.     

Control of Tryptophan Biosynthesis in Plant Tissue Cultures: Lack of Repression of Anthranilate and Tryptophan Synthetases by Tryptophan

Tobacco (cv. Xanthi and cv. Wisconsin 38), rice, carrot, tomato, and soybean tissue cultures were grown in liquid media containing L-tryptophan. The addition of tryptophan increased the cellular tryptophan levels greatly (12–2500 fold), but did not lower appreciably the levels of two tryptophan biosynthetic enzymes, anthranilate synthetase and tryptophan synthetase. However, the addition of 50 μM tryptophan to the crude enzyme extract completely inhibited the anthranilate synthetase activity while 1 mM tryptophan inhibited the tryptophan synthetase activity by only 10–20°/o. This information indicates that tryptophan biosynthesis is controlled by the feedback inhibition of anthranilate synthetase by tryptophan and not by repression of enzyme synthesis. All of the species had significant enzyme levels. Anthranilate synthetase activity could not be detected in extracts from cells grown on tryptophan unless the extracts were first passed through two G-25 Sephadex columns with a short 30 °C warming step in between, a procedure shown to remove an inhibitor of the enzyme.     

Tryptophan Biosynthesis from Indole-3-Acetic Acid by Anaerobic Bacteria from the Rumen

Microbes in ruminal contents incorporated (14)C into cells when they were incubated in vitro in the presence of [(14)C]carboxyl-labeled indole-3-acetic acid (IAA). Most of the cellular (14)C was found to be in tryptophan from the protein fractions of the cells. Pure cultures of several important ruminal species did not incorporate labeled IAA, but all four strains of Ruminococcus albus tested utilized IAA for tryptophan synthesis. R. albus did not incorporate (14)C into tryptophan during growth in medium containing either labeled serine or labeled shikimic acid. The mechanism of tryptophan biosynthesis from IAA is not known but appears to be different from any described biosynthetic pathway. We propose that a reductive carboxylation, perhaps involving a low-potential electron donor such as ferredoxin, is involved.     

A Novel Approach to Enhancing Ganoderic Acid Production by Ganoderma lucidum Using Apoptosis Induction

Ganoderma lucidum is one of most widely used herbal medicine and functional food in Asia, and ganoderic acids (GAs) are its active ingredients. Regulation of GA biosynthesis and enhancing GA production are critical to using G. lucidum as a medicine. However, regulation of GA biosynthesis by various signaling remains poorly understood. This study investigated the role of apoptosis signaling on GA biosynthesis and presented a novel approach, namely apoptosis induction, to increasing GA production. Aspirin was able to induce cell apoptosis in G. lucidum, which was identified by terminal deoxynucleotidyl transferase mediated dUPT nick end labeling assay positive staining and a condensed nuclear morphology. The maximum induction of lanosta-7,9(11), 24-trien-3α-01-26-oic acid (ganoderic acid 24, GA24) production and total GA production by aspirin were 2.7-fold and 2.8-fold, respectively, after 1 day. Significantly lower levels of GA 24 and total GAs were obtained after regular fungal culture for 1.5 months. ROS accumulation and phosphorylation of Hog-1 kinase, a putative homolog of MAPK p38 in mammals, occurred after aspirin treatment indicating that both factors may be involved in GA biosynthetic regulation. However, aspirin also reduced expression of the squalene synthase and lanosterol synthase coding genes, suggesting that these genes are not critical for GA induction. To the best of our knowledge, this is the first report showing that GA biosynthesis is linked to fungal apoptosis and provides a new approach to enhancing secondary metabolite production in fungi.     

Biosynthesis of d-Erythroascorbic Acid by Candida

Epigallocatechin 3-gallate (EGCG) has cytotoxic effects in many cancer cells. It has been reported that A549 lung cancer cells are markedly resistant to cell death induced by EGCG. In the present study, the effects of EGCG on A549 lung cancer cell growth and angiogenesis were studied. We found that EGCG dose-dependently suppressed A549 cell growth, while A549 cells were markedly resistant to cell death in vitro. Next we found that EGCG increased endostatin expression and suppressed vascular endothelial growth factor (VEGF) expression. We further studied to determine whether EGCG would suppress A549 tumor growth in nude mouse and angiogenesis. EGCG in drinking water significantly suppressed A549 tumor growth in nude mice. Histological analysis revealed that the number of CD34 positive vessels had a tendency to decrease in the tumor. In sum, EGCG had anti-proliferative effects of A549 on tumor growth and showed a tendency to suppress angiogenesis.     

A Novel Approach to Decrease Sialic Acid Expression in Cells by a C-3-modified N-Acetylmannosamine

Due to its position at the outermost of glycans, sialic acid is involved in a myriad of physiological and pathophysiological cell functions such as host-pathogen interactions, immune regulation, and tumor evasion. Inhibitors of cell surface sialylation could be a useful tool in cancer, immune, antibiotic, or antiviral therapy. In this work, four different C-3 modified N-acetylmannosamine analogs were tested as potential inhibitors of cell surface sialylation. Peracetylated 2-acetylamino-2-deoxy-3-O-methyl-d-mannose decreases cell surface sialylation in Jurkat cells in a dose-dependent manner up to 80%, quantified by flow cytometry and enzyme-linked lectin assays. High-performance liquid chromatography experiments revealed that not only the concentration of membrane bound but also of cytosolic sialic acid is reduced in treated cells. We have strong evidence that the observed reduction of sialic acid expression in cells is caused by the inhibition of the bifunctional enzyme UDP-GlcNAc-2-epimerase/ManNAc kinase. 2-Acetylamino-2-deoxy-3-O-methyl-d-mannose inhibits the human ManNAc kinase domain of the UDP-GlcNAc-2-epimerase/ManNAc kinase. Binding kinetics of the inhibitor and human N-acetylmannosamine kinase were evaluated using surface plasmon resonance. Specificity studies with human N-acetylglucosamine kinase and hexokinase IV indicated a high specificity of 2-acetylamino-2-deoxy-3-O-methyl-d-mannose for MNK. This substance represents a novel class of inhibitors of sialic acid expression in cells, targeting the key enzyme of sialic acid de novo biosynthesis.     

A High-Throughput Fatty Acid Profiling Screen Reveals Novel Variations in Fatty Acid Biosynthesis in Chlamydomonas reinhardtii and Related Algae

Analysis of fatty acid methyl esters (FAMEs) by gas chromatography (GC) is a common technique for the quantitative and qualitative analysis of acyl lipids. Methods for FAME preparation are typically time-consuming and labor-intensive and require multiple transfers of reagents and products between reaction tubes and autosampler vials. In order to increase throughput and lower the time and materials costs required for FAME preparation prior to GC analysis, we have developed a method in which 10-to-20-mg samples of microbial biomass are transferred to standard GC autosampler vials, transesterified using an emulsion of methanolic trimethylsulfonium hydroxide and hexane, and analyzed directly by GC without further sample handling. This method gives results that are essentially identical to those obtained by the more labor- and material-intensive FAME preparation methods, such as transmethylation with methanolic HCl. We applied this method to the screening of laboratory and environmental isolates of the green alga Chlamydomonas for variations in fatty acid composition. This screening method facilitated two novel discoveries. First, we identified a common laboratory strain of C. reinhardtii, CC-620, completely lacking all ω-3 fatty acids normally found in this organism and showed that this strain contains an inactivating mutation in the CrFAD7 gene, encoding the sole ω-3 desaturase activity in this organism. Second, we showed that some species of Chlamydomonas make Δ6-unsaturated polyunsaturated fatty acids (PUFA) rather than the Δ5 species normally made by the previously characterized laboratory strains of Chlamydomonas, suggesting that there is species-specific variation in the regiospecificity and substrate selectivity of front-end desaturases in this algal genus.     

Biosynthesis of Novel Exopolymers by Aureobasidium pullulans

Aureobasidium pullulans ATCC 42023 was cultured under aerobic conditions with glucose, mannose, and glucose analogs as energy sources. The exopolymer extracts produced under these conditions were composed of glucose and mannose. The molar ratio of glucose to mannose in the exopolymer extract and the molecular weight of the exopolymer varied depending on the energy source and culture time. The glucose content of exopolymer extracts formed with glucose and mannose as the carbon sources was between 91 and 87%. The molecular weight decreased from 3.5 × 10⁶ to 2.12 × 10⁶ to 0.85 × 10⁶ to 0.77 × 10⁶ with culture time. As the culture time increased, the glucose content of the exopolymer extract formed with glucosamine decreased from 55 ± 3 to 29 ± 2 mol%, and the molecular weight increased from 2.73 × 10⁶ to 4.86 × 10⁶. There was no evidence that glucosamine was directly incorporated into exopolymers. The molar ratios of glucose to mannose in exopolymer extracts ranged from 87 ± 3:13 ± 3 to 28 ± 2:72 ± 2 and were affected by the energy source added. On the basis of the results of an enzyme hydrolysis analysis of the exopolymer extracts and the compositional changes observed, mannose (a repeating unit) was substituted for glucose, which gave rise to a new family of exopolymer analogs.     

Inhibition of Phosphatidic Acid Biosynthesis by cis-9,10-Methylene Hexadecanoic Acid

We tested the effect of oral administration of fermented sake lees with lactic acid bacteria (FESLAB) on a murine model of allergic rhinitis upon immunization and nasal sensitization with ovalbumin (OVA). We used Lactobacillus paracasei NPSRIk-4 (isolated from sake lees), and L. brevis NPSRIv-8 (from fermented milk) as starter strains to produce the FESLAB. Oral FESLAB administration resulted in the development of significantly fewer sneezing symptoms than those seen in sham control animals given sterile water. We also found that FESLAB suppressed the allergen-induced degranulation of RBL2H3 rat basophilic leukemia cells.     

A Novel Red Clover Hydroxycinnamoyl Transferase Has Enzymatic Activities Consistent with a Role in Phaselic Acid Biosynthesis

Red clover (Trifolium pratense) leaves accumulate several μmol g⁻¹ fresh weight of phaselic acid [2-O-(caffeoyl)-l-malate]. Postharvest oxidation of such o-diphenols to o-quinones by endogenous polyphenol oxidases prevents breakdown of forage protein during storage. Forage crops like alfalfa (Medicago sativa) lack both polyphenol oxidase and o-diphenols, and breakdown of their protein upon harvest and storage results in economic losses and release of excess nitrogen into the environment. Understanding how red clover synthesizes o-diphenols such as phaselic acid will help in the development of forage crops utilizing this natural system of protein protection. A possible pathway for phaselic acid biosynthesis predicts a hydroxycinnamoyl transferase (HCT) capable of forming caffeoyl and/or p-coumaroyl esters with malate. Genes encoding two distinct HCTs were identified in red clover. HCT1 shares more than 75% amino acid identity with a number of well-characterized shikimate O-HCTs implicated in monolignol biosynthesis. HCT2 shares only 34% amino acid sequence identity with HCT1 and has limited sequence identity to any previously identified HCT. Expression analyses indicate that HCT1 mRNA accumulates to 4-fold higher levels in stems than in leaves, whereas HCT2 mRNA accumulates to 10-fold higher levels in leaves than in stems. Activity assays of HCT1 and HCT2 proteins expressed in Escherichia coli indicate that HCT1 transfers caffeoyl or p-coumaroyl moieties from a coenzyme A-thiolester to shikimate but not malate, whereas HCT2 transfers caffeoyl or p-coumaroyl moieties from a coenzyme A-thiolester to malate but not shikimate. Together, these results indicate that HCT1 is involved in monolignol biosynthesis and HCT2 is a novel transferase likely involved in phaselic acid biosynthesis.In contrast to many other forage legumes (e.g. alfalfa [Medicago sativa]; Jones et al., 1995), red clover (Trifolium pratense) accumulates relatively high levels of the phenylpropanoid o-diphenol phaselic acid [2-O-(caffeoyl)-l-malic acid; hereafter referred to as caffeoyl-malate or phaselic acid] in its leaves (Hatfield and Muck, 1999; Winters et al., 2008). In red clover, upon cellular disruption, phaselic acid and other o-diphenols are readily oxidized by a soluble polyphenol oxidase (PPO) to produce their corresponding o-quinones (Hatfield and Muck, 1999; Sullivan et al., 2004). The formation of such o-quinones by PPO, and the subsequent secondary reactions of these quinones, are most often associated with browning of fresh fruits and vegetables (Steffens et al., 1994), which has a negative impact on perceived quality. When preserved by ensiling, however, oxidation of o-diphenols by PPO in red clover prevents degradation of protein during storage (Sullivan et al., 2004; Sullivan and Hatfield, 2006). Although alfalfa lacks significant levels of both PPO activity and o-diphenol compounds in its leaves, red clover''s natural system of protein protection has been transferred to this forage legume by expressing a red clover PPO transgene in alfalfa and exogenously adding o-diphenol PPO substrates to the resulting tissues or tissue extracts (Sullivan et al., 2004; Sullivan and Hatfield, 2006). Because ruminant animals poorly utilize degraded protein, adaptation of the PPO system to alfalfa and other forage crops would have substantial positive economic and environmental impacts (Sullivan and Hatfield, 2006). Unfortunately, lack of system components in these forage crops, especially the o-diphenol PPO substrates, presents a challenge to practical adaptation of this natural system of protein preservation. Consequently, understanding how red clover is able to accumulate o-diphenols such as phaselic acid will be a key step to adapt the PPO/o-diphenol system to a wide range of economically important forage crops.The biosynthetic pathways whereby red clover synthesizes and accumulates phaselic acid and other o-diphenols have not been defined. However, in the Brassicaceae, hydroxycinnamoyl esters with malic acid can be made via the action of sinapoyl-Glc:malate sinapoyltransferase (SMT; EC 2.3.1), which is capable of transferring a hydroxycinnamoyl moiety from a hydroxycinnamoyl-Glc ester to a malic acid acceptor. In Arabidopsis (Arabidopsis thaliana), SNG1 (for sinapoylglucose accumulator 1), which encodes the enzyme, has been shown to be responsible for the accumulation of sinapoylmalate in seeds and leaves (Lehfeldt et al., 2000). An SMT from radish (Raphanus sativus), presumably the homolog of the Arabidopsis SNG1 gene product, has been purified to apparent homogeneity and characterized (Grawe et al., 1992). The purified enzyme is capable of utilizing sinapoyl-, feruloyl-, caffeoyl-, and to a lesser extent p-coumaroyl-Glc esters to form the corresponding malic acid esters, suggesting that it is responsible for the accumulation of these esters in vivo. In contrast, in many plants, formation of certain hydroxycinnamoyl esters is often mediated by a member of the BAHD transferase family (D''Auria, 2006) that utilize a CoA thiolester hydroxycinnamoyl donor. Some of the best characterized of these hydroxycinnamoyl transferases (HCTs) are those associated with the biosynthesis of monolignols (Hoffmann et al., 2003, 2004; Shadle et al., 2007). These are capable of transferring p-coumaroyl or caffeoyl moieties from the respective CoA thiolesters to form 5-O-esters with shikimic acid or, to a lesser extent, 3-O-esters with quinic acid. Separable enzymatic activities capable of transferring a p-coumaroyl moiety to either shikimate/quinate or to 4′-hydroxyphenyllactate in basil (Ocimum basilicum) peltate gland extracts have been identified, although genes encoding these activities have not been cloned (Gang et al., 2002). Niggeweg et al. (2004) used gene-silencing experiments to definitively demonstrate that a hydroxycinnamoyl-CoA:quinate hydroxycinnamoyl transferase (HQT) is responsible for chlorogenic acid accumulation in the Solanaceae. Although phaselic acid biosynthesis in red clover could be via a pathway utilizing SMT, lack of an apparent SNG1 homolog in a collection of red clover EST sequences derived from leaves and young plants suggests otherwise (see “Discussion”). Therefore, pathways in red clover for the biosynthesis of phaselic acid utilizing one or more BAHD family transferase (Fig. 1) should be considered. In these proposed pathways, Phe would be converted to p-coumaroyl-CoA by the sequential action of Phe ammonia lyase (PAL), cinnamate-4-hydroxylase (C4H), and 4-coumarate:CoA ligase (4CL). The action of one or more specific HCTs and one or more p-coumarate 3′-hydroxylases (C3Hs) would then result in the formation of phaselic acid.Open in a separate windowFigure 1.Possible pathways for phaselic acid biosynthesis in red clover. Proposed pathway enzymes for the production of phaselic acid include PAL, 4CL, hydroxycinnamoyl:shikimate transferase (HCT-S), hydroxycinnamoyl:malate transferase (HCT-M), and C3H. The branch point at p-coumaroyl-CoA represents two alternative pathways. For simplicity, not all reactants and products are shown.Existing literature suggests that C3H enzymes, which are cytochrome P450 enzymes (CYP98A subfamily), do not directly hydroxylate p-coumaric acid to caffeic acid but rather act on p-coumaroyl ester derivatives. For example, the enzyme from Arabidopsis hydroxylates shikimic and quinic acid esters of p-coumaric acid but only poorly or not at all p-coumaric acid or its Glc or CoA esters (Schoch et al., 2001; Franke et al., 2002). Thus, one model of phaselic acid biosynthesis is the formation of 2-O-(p-coumaroyl)-l-malic acid (hereafter referred to as p-coumaroyl-malate) by a HCT and its subsequent hydroxylation by a C3H enzyme capable of utilizing the malic acid ester as a substrate (Fig. 1, bottom, red pathway). An alternative model would require at least two HCT activities for phaselic acid biosynthesis (Fig. 1, top, blue pathway). The first activity would form a substrate suitable for hydroxylation (e.g. p-coumaroyl-shikimate, since several characterized C3H enzymes appear to favor this substrate [Schoch et al., 2001; Franke et al., 2002; Gang et al., 2002; Morant et al., 2007]). Following hydroxylation to the caffeoyl derivative by a C3H, the first HCT activity could synthesize caffeoyl-CoA via its reverse reaction (Hoffmann et al., 2003; Niggeweg et al., 2004). A second HCT activity would then transfer the caffeoyl moiety to malic acid to form phaselic acid. Both pathways predict a transferase capable of transferring a hydroxycinnamoyl moiety (either p-coumaroyl or caffeoyl) to malic acid. Also, these pathways are consistent with the observation that, at least in vitro, several characterized HCT enzymes are capable of transfer reactions utilizing either p-coumaroyl- or caffeoyl-CoA (Hoffmann et al., 2003; Niggeweg et al., 2004). The identification and characterization of two distinct HCTs from red clover, one of which has properties consistent with a role in phaselic acid biosynthesis, are reported here.     

Amino Acid Biosynthesis by Isolated Chloroplasts during Photosynthesis

The pool sizes of the common amino acids in purified intact chloroplasts from Vicia faba L. were measured (nanomoles per milligram chlorophyll). The three amino acids present in the highest concentrations were glutamate, aspartate, and threonine. Alanine, serine, and glycine were each present at levels between 15 and 20 nanomoles per milligram chlorophyll and 13 other amino acids were detectable at levels below 10.     

Biosynthesis of jasmonic Acid by several plant species

Six plant species metabolized ¹⁸O-labeled 12-oxo-cis,cis-10,15-phytodienoic acid (12-oxo-PDA) to short chain cyclic fatty acids. The plant species were corn (Zea mays L.), eggplant (Solanum melongena L.), flax (Linum usitatissimum L.), oat (Avena sativa L.), sunflower (Helianthus annuus L.), and wheat (Triticum aestivum L.). Among the products was jasmonic acid, a natural plant constituent with growth-regulating properties. The pathway is the same as the one recently reported by us for jasmonic acid synthesis in Vicia faba L. pericarp. First, the ring double bond of 12-oxo-PDA is saturated; then β-oxidation enzymes remove six carbons from the carboxyl side chain of the ring. Substrate specificity studies indicated that neither the stereochemistry of the side chain at carbon 13 of 12-oxo-PDA nor the presence of the double bond at carbon 15 was crucial for either enzyme step. The presence of enzymes which convert 12-oxo-PDA to jasmonic acid in several plant species indicates that this may be a general metabolic pathway in plants.     

Epitope Prediction by Novel Immunoinformatics Approach: A State-of-the-art Review

International Journal of Peptide Research and Therapeutics - Immunoinformatics is a science that helps to create significant immunological information using bioinformatics softwares and...     

用于串联质谱鉴定多肽的计量方法

目前已有多种对串联质谱与数据库中多肽的理论质谱的一致性进行评估的高通量计量算法用于鸟枪法蛋白质组学 (shotgunproteomics)研究。然而这些方法操作时存在大量错误的多肽鉴定。这里提出一种新的串联质谱识别多肽序列的计量算法。该算法综合考虑了串联质谱中不同离子出现的概率、多肽的酶切位点数、理论离子与实验离子的匹配程度和匹配模式。对大容量的串联质谱数据集的测试表明 ,根据算法开发的软件PepSearch比目前最常用的软件SEQUEST有更好的鉴定准确性。PepSearch可从http : compbio.sibsnet.org projects pepsearch下载。     

Type II Fatty Acid Biosynthesis, a New Approach in Antimalarial Natural Product Discovery

Malaria, one of the most problematic infectious diseases worldwide, is on the rise. The absence of an effective vaccine and the spread of drug-resistant strains of Plasmodium clearly indicate the necessity for the development of new chemotherapeutic agents and the identification of novel targets. The recent discovery of a relict, non-photosynthetic plastid-like organelle, the so-called apicoplast, in Plasmodium has opened up new avenues in malaria research. It also initiated the Plasmodium falciparum genome sequencing project, which revealed a number of biochemical pathways previously unknown to Plasmodium, i.e. cytosolic shikimate pathway, apicoplastic type II fatty acid, non-mevalonate isoprene and haem biosyntheses. Since these vital biosynthetic processes are absent in humans or fundamentally different from those found in humans, they represent excellent targets for pharmaceutical interventions. We are interested in the type II fatty acid synthase (FAS II) system of malaria parasite and focus on the FabI enzyme, the only known enoyl-ACP reductase in Plasmodium involved in the final reduction step of the fatty acid chain elongation cycle. Here we describe the general aspects of fatty acid biosynthesis, its essentiality to the malaria parasite and our continuing efforts to discover in Turkish medicinal plants natural antimalarial agents, which specifically target the plasmodial FabI enzyme.Phytochemical Society of Europe (PSE)-Pierre Fabre Prize 2004 Lecture