Engineered reversal of the β-oxidation cycle for the synthesis of fuels and chemicals

Advanced (long-chain) fuels and chemicals are generated from short-chain metabolic intermediates through pathways that require carbon-chain elongation. The condensation reactions mediating this carbon-carbon bond formation can be catalysed by enzymes from the thiolase superfamily, including β-ketoacyl-acyl-carrier protein (ACP) synthases, polyketide synthases, 3-hydroxy-3-methylglutaryl-CoA synthases, and biosynthetic thiolases. Pathways involving these enzymes have been exploited for fuel and chemical production, with fatty-acid biosynthesis (β-ketoacyl-ACP synthases) attracting the most attention in recent years. Degradative thiolases, which are part of the thiolase superfamily and naturally function in the β-oxidation of fatty acids, can also operate in the synthetic direction and thus enable carbon-chain elongation. Here we demonstrate that a functional reversal of the β-oxidation cycle can be used as a metabolic platform for the synthesis of alcohols and carboxylic acids with various chain lengths and functionalities. This pathway operates with coenzyme A (CoA) thioester intermediates and directly uses acetyl-CoA for acyl-chain elongation (rather than first requiring ATP-dependent activation to malonyl-CoA), characteristics that enable product synthesis at maximum carbon and energy efficiency. The reversal of the β-oxidation cycle was engineered in Escherichia coli and used in combination with endogenous dehydrogenases and thioesterases to synthesize n-alcohols, fatty acids and 3-hydroxy-, 3-keto- and trans-Δ(2)-carboxylic acids. The superior nature of the engineered pathway was demonstrated by producing higher-chain linear n-alcohols (C?≥?4) and extracellular long-chain fatty acids (C?>?10) at higher efficiency than previously reported. The ubiquitous nature of β-oxidation, aldehyde/alcohol dehydrogenase and thioesterase enzymes has the potential to enable the efficient synthesis of these products in other industrial organisms.     

A chain initiation factor common to both modular and aromatic polyketide synthases.

Antibiotic-producing polyketide synthases (PKSs) are enzymes responsible for the biosynthesis in Streptomyces and related filamentous bacteria of a remarkably broad range of bioactive metabolites, including antitumour aromatic compounds such as mithramycin and macrolide antibiotics such as erythromycin. The molecular basis for the selection of the starter unit on aromatic PKSs is unknown. Here we show that a component of aromatic PKS, previously named 'chain-length factor', is a factor required for polyketide chain initiation and that this factor has decarboxylase activity towards malonyl-ACP (acyl carrier protein). We have re-examined the mechanism of initiation on modular PKSs and have identified as a specific initiation factor a domain of previously unknown function named KSQ, which operates like chain-length factor. Both KSQ and chain-length factor are similar to the ketosynthase domains that catalyse polyketide chain extension in modular multifunctional PKSs and in aromatic PKSs, respectively, except that the ketosynthase domain active-site cysteine residue is replaced by a highly conserved glutamine in KSQ and in chain-length factor. The glutamine residue is important both for decarboxylase activity and for polyketide synthesis.     

A new class of homoserine lactone quorum-sensing signals

Quorum sensing is a term used to describe cell-to-cell communication that allows cell-density-dependent gene expression. Many bacteria use acyl-homoserine lactone (acyl-HSL) synthases to generate fatty acyl-HSL quorum-sensing signals, which function with signal receptors to control expression of specific genes. The fatty acyl group is derived from fatty acid biosynthesis and provides signal specificity, but the variety of signals is limited. Here we show that the photosynthetic bacterium Rhodopseudomonas palustris uses an acyl-HSL synthase to produce p-coumaroyl-HSL by using environmental p-coumaric acid rather than fatty acids from cellular pools. The bacterium has a signal receptor with homology to fatty acyl-HSL receptors that responds to p-coumaroyl-HSL to regulate global gene expression. We also found that p-coumaroyl-HSL is made by other bacteria including Bradyrhizobium sp. and Silicibacter pomeroyi. This discovery extends the range of possibilities for acyl-HSL quorum sensing and raises fundamental questions about quorum sensing within the context of environmental signalling.     

何首乌中一种Ⅲ型PKS基因的克隆及生物信息学分析

Ⅲ型聚酮合酶即查耳酮合酶超家族,能催化生成一系列结构各异、具有不同生理活性、含有查耳酮合酶基本骨架的植物次生代谢产物。根据不同植物Ⅲ型PKSs基因的保守序列,设计简并引物,采用RT - PCR和RACE技术,首次从传统中药材何首乌(Polygonum multiflorum Thunb.)中克隆到一种Ⅲ型PKS基因,其cDNA全长1228bp, 编码379个氨基酸,命名为FmPKS (GenBank登录号: GQ411431)。该基因含有三个内含子, 与迄今报道的绝大部分Ⅲ型PKS含有一个内含子不同,而与最近报道的虎杖中克隆的PcPKS2基因相同。通过生物信息学方法对其编码蛋白的序列进行同源性分析,构建了系统进化树,并对其等电点、疏水性及二级结构、跨膜区域等理化性质进行了初步预测,为进一步研究其功能奠定了基础。     

Convergence of 9-cis retinoic acid and peroxisome proliferator signalling pathways through heterodimer formation of their receptors.

Peroxisomes are cytoplasmic organelles which are important in mammals in modulation of lipid homeostasis, including the metabolism of long-chain fatty acids and conversion of cholesterol to bile salts (reviewed in refs 1 and 2). Amphipathic carboxylates such as clofibric acid have been used in man as hypolipidaemic agents and in rodents they stimulate the proliferation of peroxisomes. These agents, termed peroxisome proliferators, and all-trans retinoic acid activate genes involved in peroxisomal-mediated beta-oxidation of fatty acids. Here we show that the receptor activated by peroxisome proliferators and the retinoid X receptor-alpha (ref. 6) form a heterodimer that activates acyl-CoA oxidase gene expression in response to either clofibric acid or the retinoid X receptor-alpha ligand, 9-cis retinoic acid, an all-trans retinoic acid metabolite; simultaneous exposure to both activators results in a synergistic induction of gene expression. These data demonstrate the coupling of the peroxisome proliferator and retinoid signalling pathways and provide evidence for a physiological role for 9-cis retinoic acid in modulating lipid metabolism.     

不同类型脂肪酸对SD大鼠血清生化指标及胰岛素抵抗的影响

目的分析中链饱和脂肪酸(MC-SFA,MCF组)、长链饱和脂肪酸(LC-SFA,LCF组)、n-6多不饱和脂肪酸(n-6PUFA,SUF组)和n-3多不饱和脂肪酸(n-3PUFA,TUF组)四种脂肪酸对大鼠血清生化指标及胰岛素抵抗的影响。方法雄性SD大鼠40只随机分为5组,对照组给予普通日粮,高脂组给予脂肪热量比相同的高脂日粮。喂养10w,每18d测定空腹血糖(GLU)、甘油三酯(TG)、高密度脂蛋白胆固醇(HDL-c)、总胆固醇(TC)和血清胰岛素水平,根据胰岛素敏感性指数(ISI)=㏑1/(FPG×FINS)评定大鼠的胰岛素敏感性。结果10w后,LCF组和SUF组体重显著高于对照组和其它高脂组;LCF组和对照组血清TG显著高于其它高脂组(P0.05);LCF组血清TC显著高于对照组和其它高脂组(P0.05);高脂组血清HDL-c均显著低于对照组(P0.05)并以TUF组下降幅度最大;LCF组血清胰岛素显著高于对照组(P0.05);LCF组和TUF组ISI显著低于对照组(P0.05);各组间血糖无明显差异(P0.05)。结论不同类型脂肪酸对大鼠体重、血清生化指标及胰岛素抵抗的影响有显著差异。     

Molecular organic geochemical peculiarities of lacustrine core sediments in Fildes Peninsula, King George Island, Antarctica

The peculiarities of lipids in lacustrine core sediments from Fildes Peninsula, King George Island, Antarctica, are reported. The origin of high-molecular-weight n-alkanes, alkenes,fatty acids, alcohols is supposed to be related to the abundant moss occurring in the sediments.Abundant iso-and anteiso-fatty acids that occur in the sediments indicate a relatively strong bacterial activity in non-ice-cover zone than in other regions in Antarctica. The C18:2 unsaturated fatty acids mainly originate from autochthonous algae in the sediment pool, and the C18:2/C18:0ratios in the profile are controlled more by paleotemperatures than source assemblies. Long-chain alkenones were identified in freshwater lacustrine sediment in Antarctica for the first time, of which Prymnesiophyceae is assumed to be the source organism. High relative abundance of C37:4honologue in long-chain alkenone well correlates to the severely cold climate in Antarctica.     

Free fatty acids regulate insulin secretion from pancreatic beta cells through GPR40

Diabetes, a disease in which carbohydrate and lipid metabolism are regulated improperly by insulin, is a serious worldwide health issue. Insulin is secreted from pancreatic beta cells in response to elevated plasma glucose, with various factors modifying its secretion. Free fatty acids (FFAs) provide an important energy source as nutrients, and they also act as signalling molecules in various cellular processes, including insulin secretion. Although FFAs are thought to promote insulin secretion in an acute phase, this mechanism is not clearly understood. Here we show that a G-protein-coupled receptor, GPR40, which is abundantly expressed in the pancreas, functions as a receptor for long-chain FFAs. Furthermore, we show that long-chain FFAs amplify glucose-stimulated insulin secretion from pancreatic beta cells by activating GPR40. Our results indicate that GPR40 agonists and/or antagonists show potential for the development of new anti-diabetic drugs.     

Vitamin E modulates the lipoxygenation of arachidonic acid in leukocytes

The arachidonic acid released from cellular phospholipids of specifically stimulated platelets and leukocytes is oxygenated enzymatically by two major pathways. A complex cycloxygenase converts some of the free arachidonic acid to labile endoperoxides that are transformed to prostaglandins, thromboxanes and prostacyclin (PGI2). Lipoxygenases convert part of the arachidonic acid to unstable hydroperoxy-eicosatetraenoic acids (OOHETEs) that are transformed to monohydroxyeicosatetraenoic acids (HETEs), oligohydroxy-eicosatetraenoic or -eicostatrienoic acids such as di-HETEs and tri-HETEs, and, in some instances, more complex humoral mediators, including slow-reacting substances. Both the nature of the HETEs and the ratio of the HETEs to the cyclo-oxygenase products are specific characteristics of each type of cell. In human neutrophils, the sum of the lipoxygenase products 5-HETE, 11-HETE and 5,12-di-HETE substantially exceeds the total amount of PGE2 and other cyclo-oxygenase metabolites that are generated concurrently, and the endogenous lipoxygenase products regulate neutrophil function. The present data indicate that vitamin E (alpha-tocopherol) bidirectionally modulates the activity of the lipoxygenase pathway of human neutrophils in vitro. Normal plasma concentrations of alpha-tocopherol enhance the lipoxygenation of arachidonic acid, whereas higher concentrations of alpha-tocopherol exert a suppressive effect that is consistent with its role as a hydroperoxide scavenger.     

对氨基苯甲酸生物合成基因pabAB的缺失对抗生素FR-008生物合成的影响

抗生素FR-008是由链霉菌FR-008产生的一种七烯大环内酯类抗真菌抗生素,它以对氨基苯甲酸(PABA)为起始单位,在I型聚酮合酶(PKS)的催化下合成聚酮内酯环.前期生物合成基因簇序列测定发现了可能的对氨基苯甲酸生物合成基因(pabAB),编码4-氨基-4-脱氧-分支酸(ADC)合成酶.通过同框缺失实验获得pabAB发生缺失的基因置换突变株BLQ-1并通过聚合酶链式反应(PCR)扩增进行了验证.高效液相色谱(HPLC)分析和生物测定证实突变菌株BLQ-1丧失了合成抗生素FR-008的能力.这种产量的丧失可以通过回补克隆的pabAB基因或喂养外源PABA得到回复.实验证明,pabAB负责对氨基苯甲酸的合成,是抗生素FR-008生物合成的必需基因.     

Simulation experiments for evolution of fatty acids in immature source rocks

The anhydrous, hydrous and bitumen-extrac- ted simulations were carried out for the immature source rocks from the Liaohe sag. It has been shown from the result that with increasing temperature in simulation experiments, the fatty acids content decreased at first and then increased. The decrease of fatty acids in immature rocks is presumably related to alkanes generation in immature oils, whilst the increase may be related to the fact that some additional fatty acids are generated from kerogen and the tightly bound fatty acids in kerogen are released as bound fatty acids in kerogen and unbound fatty acids in bitumen. The fact that the bitumen generated from kerogen contains fatty acids has demonstrated that some bound and tightly bound fatty acids in kerogen can be transferred into bitumen. The preferential fatty acids in the immature source rocks are found to be mono-carboxylic acids with longer chains, whilst krogen contains relatively more di-carboxylic acids. It has been found that the fatty acids in immature source rocks can be changed from that with more longer chains to that with more shorter chains when evolution extent has been increased. Based on simulation results and the fact that the majority of fatty acids in immature oils are those with longer chains, it is inferred that the contribution of fatty acids to forming alkanes in immature oils mainly takes place at the evolution stage with R₀ <0.6%. The simulation experiments have also demonstrated that H₂O could promote the generation of fatty acids with more di-carboxylic acids and delay alkanes formation from fatty acids.     

A new pathway for polyketide synthesis in microorganisms.

Chalcone synthases, which biosynthesize chalcones (the starting materials for many flavonoids), have been believed to be specific to plants. However, the rppA gene from the Gram-positive, soil-living filamentous bacterium Streptomyces griseus encodes a 372-amino-acid protein that shows significant similarity to chalcone synthases. Several rppA-like genes are known, but their functions and catalytic properties have not been described. Here we show that a homodimer of RppA catalyses polyketide synthesis: it selects malonyl-coenzyme-A as the starter, carries out four successive extensions and releases the resulting pentaketide to cyclize to 1,3,6,8-tetrahydroxynaphthalene (THN). Site-directed mutagenesis revealed that, as in other chalcone synthases, a cysteine residue is essential for enzyme activity. Disruption of the chromosomal rppA gene in S. griseus abolished melanin production in hyphae, resulting in 'albino' mycelium. THN was readily oxidized to form 2,5,7-trihydroxy-1,4-naphthoquinone (flaviolin), which then randomly polymerized to form various coloured compounds. THN formed by RppA appears to be an intermediate in the biosynthetic pathways for not only melanins but also various secondary metabolites containing a naphthoquinone ring. Therefore, RppA is a chalcone-synthase-related synthase that synthesizes polyketides and is found in the Streptomyces and other bacteria.     

Homology between Streptomyces genes coding for synthesis of different polyketides used to clone antibiotic biosynthetic genes

Many important antibiotics such as tetracyclines, erythromycin, adriamycin, monensin, rifamycin and avermectins are polyketides. In their biosynthesis, multifunctional synthases catalyse iterated condensation of thio-esters derived from acetate, propionate or butyrate to yield aliphatic chains of varying length and carrying different alkyl substituents. Subsequent modifications, including aromatic or macrolide ring closure or specific methylations or glycosylations, generate further chemical diversity. It has been suggested that, if different polyketide synthases had a common evolutionary origin, cloned DNA coding for one synthase might be used as a hybridization probe for the isolation of others. We show here that this is indeed possible. Study of a range of such synthase genes and their products should help to elucidate what determines the choice and order of condensation of different residues in polyketide assembly, and might yield, by in vitro recombination or mutagenesis, synthase genes capable of producing novel antibiotics. Moreover, because genes for entire antibiotic pathways are usually clustered in Streptomyces, cloned polyketide synthase genes are valuable in giving access to groups of linked biosynthetic genes.     

长链脂肪酸体系固—液相变动力学参数的求解

用Kinssinger和Ozawa法处理长链脂肪酸体系固－液相变的DSC数据,估算出其相变反应的动力学参数,两种动力学计算结果均显示,长链脂肪酸固－液相变的表观活化能与（平均）分子量有关。     

Long-chain branched/cyclic alkanes in recent sediment of Lake Fuxian and their environmental implications

Lake Fuxian is a large, deep, and oligotrophic freshwater lake. In recent sediment of this lake, a series of branched and cyclic alkanes, including branched alkanes with one or two quaternary carbon atoms （C2n compounds）, alkylcycloheptane, and alkylcyclohexane, were detected in high abundance. For each homolog of long-chain branched/ cyclic alkanes, molecules with only an odd or even carbon number were present in the sediment. The abundance vari- ation of each compound homolog corresponded to those of other compound homolog in the section, indicating the same origin of these compounds. The concentrations of long-chain branched/cyclic alkanes in the sediment profile exhibited variations similar to those of phytoplankton biomarkers, such as 3-methylJalkanes, short-chain odd carbon n-alkanes, hopene, polyunsaturated fatty acids, phytol, sterols, and long-chain alkyl diols, but slightly different from those of long-chain odd carbon n-alkanes, which are ubiquitous biomarkers for higher plants. Therefore, the Can compounds and long-chain cyclic alkanes in the lake sediment were most likely produced by algae and bacteria in the water, primarily, by the heterotrophic bacteria in the moderately oxygenated waters, which flourishing might be the results of specific water environments in Lake Fuxian.     

几种油酸亚油酸的定性定量分析

用场解吸质谱和HP6890系列GC气相色谱仪、FFAP酸性毛细管色谱柱分析了国产工业级 和试剂能油酸以及生物级的亚油酸的组成。结果表明,上述油酸和亚油酸产品都是油酸和亚油酸为主的 脂肪酸混合物,但工业级油酸具有较宽的组成范围。这些结果能为应用于高水基液压液的脂肪酸产品的 选取提供技术基础。     

Evolution and metabolic significance of the urea cycle in photosynthetic diatoms

Diatoms dominate the biomass of phytoplankton in nutrient-rich conditions and form the basis of some of the world's most productive marine food webs. The diatom nuclear genome contains genes with bacterial and plastid origins as well as genes of the secondary endosymbiotic host (the exosymbiont), yet little is known about the relative contribution of each gene group to diatom metabolism. Here we show that the exosymbiont-derived ornithine-urea cycle, which is similar to that of metazoans but is absent in green algae and plants, facilitates rapid recovery from prolonged nitrogen limitation. RNA-interference-mediated knockdown of a mitochondrial carbamoyl phosphate synthase impairs the response of nitrogen-limited diatoms to nitrogen addition. Metabolomic analyses indicate that intermediates in the ornithine-urea cycle are particularly depleted and that both the tricarboxylic acid cycle and the glutamine synthetase/glutamate synthase cycles are linked directly with the ornithine-urea cycle. Several other depleted metabolites are generated from ornithine-urea cycle intermediates by the products of genes laterally acquired from bacteria. This metabolic coupling of bacterial- and exosymbiont-derived proteins seems to be fundamental to diatom physiology because the compounds affected include the major diatom osmolyte proline and the precursors for long-chain polyamines required for silica precipitation during cell wall formation. So far, the ornithine-urea cycle is only known for its essential role in the removal of fixed nitrogen in metazoans. In diatoms, this cycle serves as a distribution and repackaging hub for inorganic carbon and nitrogen and contributes significantly to the metabolic response of diatoms to episodic nitrogen availability. The diatom ornithine-urea cycle therefore represents a key pathway for anaplerotic carbon fixation into nitrogenous compounds that are essential for diatom growth and for the contribution of diatoms to marine productivity.     

小链霉菌HCCB10043敲除硫酯酶基因的工程菌株构建及其代谢产物的研究

小链霉菌(Streptomyces parvus)HCCB10043的主要代谢产物为脂肽类化合物A21978C,其基因组序列中包括了非核糖体肽合成酶(NRPS non ribosomal peptide synthetase)、聚酮合酶(PKS polyketide synthases)以及NRPS-PKS混合的多酶体系基因簇,它们的共同特点是在代谢产物生物合成簇中连接有一个硫酯酶域,即TE(thioesterase)domain.硫酯酶可以使已经合成的化合物链的合成过程终止,并且具有水解释放成熟脂肽以及环化线性脂肽链的功能.通过对联二吡啶类代谢产物合成簇中TE基因的敲除构得工程菌株,工程菌发酵结果表明联二吡啶类代谢产物产量减少.     

自养小球藻转化为异养代谢生长后细胞的超微结构与相关生化组成

利用细胞培养技术转化绿色自养的小球藻(Cholrella protothecoides)进行异养生长代谢.酶法分析反映,异养转化过程中细胞培养液中葡萄糖的利用率很高。转化后的细胞光合片层消失,叶绿体同时消失,细胞被一些大的酯肪泡填充,异养藻细胞的细胞壁也比原自养藻细胞加厚,而且细胞表而发生皱缩现象。再次将异养藻细胞置于自养生长条件下,细胞的光合片层和叶绿体结构又得以重建。生化分析显示,经异养转化后藻细胞蛋白质含量下降,为原绿色自养细胞的1/5;相反脂肪含量大幅度增加,是原初的4.4倍,达到细胞干重的72.％。异养藻细胞样品各氨某酸含量都低于自养藻细胞样品,前者以谷氨酸含量较高,后者含甘氨酸最多。在自养藻细胞样品中亚油酸的相对含量最高,为56.50％;转化为异养生长后变成油酸的相对含量占优势,达69.36％,说明异养转作用可明显降低细胞中脂防酸的不饱和程度。