The Aspergillus nidulans enzyme TdiB catalyzes prenyltransfer to the precursor of bioactive asterriquinones

The asterriquinones represent a class of ascomycete metabolic products whose significance stems from remarkable and useful pharmacological activities, among those antiretroviral (e.g., against the HI-virus), antitumor, and antidiabetes properties. Recently, the first genetic locus for an asterriquinone, the clustered terrequinone genes tdiA-E, was identified during a genome-wide screen in Aspergillus nidulans for "orphan" natural product biosynthesis loci. Here, we describe overexpression and characterization of TdiB, which catalyzes the reverse prenylation event during terrequinone A biosynthesis, which is the transfer of dimethylallyl diphosphate to carbon atom 2' of the intermediate didemethylasterriquinone D, to yield asterriquinone C-1. TdiB does not depend on the presence of divalent metal cations for catalysis and lacks the canonical prenyl diphosphate binding motif (D/N)DXXD.     

Terrequinone A biosynthesis through L-tryptophan oxidation, dimerization and bisprenylation

The antitumor fungal metabolite terrequinone A, identified in extracts of Aspergillus sp., is biosynthesized by the five-gene cluster tdiA-tdiE. In this work, we have overproduced all five proteins (TdiA-TdiE) in the bacterial host Escherichia coli, fully reconstituting the biosynthesis of terrequinone A. This pathway involves aminotransferase activity, head-to-tail dimerization and bisprenylation of the scaffold to yield the benzoquinone natural product. We have established that TdiD is a pyridoxal-5'-phosphate-dependent L-tryptophan aminotransferase that generates indolepyruvate for an unusual nonoxidative coupling by the tridomain nonribosomal peptide synthetase TdiA. TdiC, an NADH-dependent quinone reductase, generates the nucleophilic hydroquinone for two distinct rounds of prenylation by the single prenyltransferase TdiB. TdiE is required to shunt the benzoquinone away from an off-pathway monoprenylated species by an as yet unknown mechanism. Overall, we have biochemically characterized the complete biosynthetic pathway to terrequinone A, highlighting the nonoxidative dimerization pathway and the unique asymmetric prenylation involved in its maturation.     

Aspergillus nidulans natural product biosynthesis is regulated by mpkB, a putative pheromone response mitogen-activated protein kinase

The Aspergillus nidulans putative mitogen-activated protein kinase encoded by mpkB has a role in natural product biosynthesis. An mpkB mutant exhibited a decrease in sterigmatocystin gene expression and low mycotoxin levels. The mutation also affected the expression of genes involved in penicillin and terrequinone A synthesis. mpkB was necessary for normal expression of laeA, which has been found to regulate secondary metabolism gene clusters.     

Rv0989c encodes a novel (E)-geranyl diphosphate synthase facilitating decaprenyl diphosphate biosynthesis in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) has a highly complex cell wall, which is required for both bacterial survival and infection. Cell wall biosynthesis is dependent on decaprenyl diphosphate as a glyco-carrier, which is hence an essential metabolite in this pathogen. Previous biochemical studies indicated (E)-geranyl diphosphate (GPP) is required for the synthesis of decaprenyl diphosphate. Here we demonstrate that Rv0989c encodes the “missing” GPP synthase, representing the first such enzyme to be characterized from bacteria, and which presumably is involved in decaprenyl diphosphate biosynthesis in Mtb. Our investigation also has revealed previously unrecognized substrate plasticity of the farnesyl diphosphate synthases from Mtb, resolving previous discrepancies between biochemical and genetic studies of cell wall biosynthesis.     

1.55 Å-resolution structure of ent-copalyl diphosphate synthase and exploration of general acid function by site-directed mutagenesis

Background

The diterpene cyclase ent-copalyl diphosphate synthase (CPS) catalyzes the first committed step in the biosynthesis of gibberellins. The previously reported 2.25 Å resolution crystal structure of CPS complexed with (S)-15-aza-14,15-dihydrogeranylgeranyl thiolodiphosphate (1) established the αβγ domain architecture, but ambiguities regarding substrate analog binding remained.

Method

Use of crystallization additives yielded CPS crystals diffracting to 1.55 Å resolution. Additionally, active site residues that hydrogen bond with D379, either directly or through hydrogen bonded water molecules, were probed by mutagenesis.

Results

This work clarifies structure–function relationships that were ambiguous in the lower resolution structure. Well-defined positions for the diphosphate group and tertiary ammonium cation of 1, as well as extensive solvent structure, are observed.

Conclusions

Two channels involving hydrogen bonded solvent and protein residues lead to the active site, forming hydrogen bonded “proton wires” that link general acid D379 with bulk solvent. These proton wires may facilitate proton transfer with the general acid during catalysis. Activity measurements made with mutant enzymes indicate that N425, which donates a hydrogen bond directly to D379, and T421, which hydrogen bonds with D379 through an intervening solvent molecule, help orient D379 for catalysis. Residues involved in hydrogen bonds with the proton wire, R340 and D503, are also important. Finally, conserved residue E211, which is located near the diphosphate group of 1, is proposed to be a ligand to Mg^2 + required for optimal catalytic activity.

General significance

This work establishes structure–function relationships for class II terpenoid cyclases.     

不同花期‘西伯利亚’百合花瓣单萜合成途径转录组分析

以‘西伯利亚’百合（Lilium ‘Siberia’）花蕾期、半开期、盛开期、衰败期的花瓣为材料,利用RNA-seq技术对其转录组进行高通量测序,分析单萜合成途径中差异表达的基因并阐明其分子机制。结果显示,‘西伯利亚’百合通过转录组测序分析共得到56.28 Gb clean base,223.40 Mb clean reads和124 233个unigene,其中35 749个基因得到注释。萜骨架合成途径中的基因表达水平在不同花期表现出显著差异。其中,甲基赤藓糖醇磷酸（MEP）中的1-脱氧-D-木酮糖-5-磷酸合成酶（DXS）、1-脱氧-D-木酮糖-5-磷酸还原异构酶（DXR）、4-羟基-3-甲丁-2-烯基二磷酸合成酶（HDS）、4-羟基-3-甲丁-2烯基二磷酸还原酶（HDR）、牻牛儿基二磷酸合成酶（GPS）基因的表达水平随花期变化呈先升高后降低的趋势。罗勒烯合成酶（OCS）基因表现出相似变化规律,在盛开期表达量最高。甲羟戊酸（MVA）途径中的3-羟基-3-甲基戊二酸单酰辅酶A还原酶（HMGR）的基因表达同样出现先升高后降低的趋势。单萜合成下游的分支途径中,茄尼基二磷酸合成酶（SDS）、牻牛儿基牻牛儿基二磷酸合成酶（GGDR）基因的表达则出现相反的趋势,在盛开期的表达量最低。研究结果表明MEP途径中的关键基因可随花期变化规律性的表达,以调控单萜的生物合成,在盛开期有较高释放量,且盛开期MVA途径的活化以及泛醌和萜醌代谢支路基因的低表达也促进了单萜的生物合成。     

法呢基焦磷酸(FPP)的生物合成及其分子调控

法呢基焦磷酸合酶作为异戊二烯途径中的重要调节酶,是许多萜类物质的合成前体。FPS的cDNA克隆在许多生物体中也已得到了分离并进行了表达特性研究。从FPP的生物合成途径入手,对FPP生物学特性、FPS酶基因调控的相关信息进行了综述,同时对FPS在基因工程方面的应用进行了展望。     

Construction and analysis of EST libraries of the trans-polyisoprene producing plant, Eucommia ulmoides Oliver

Eucommia ulmoides Oliver is one of a few woody plants capable of producing abundant quantities of trans-polyisoprene rubber in their leaves, barks, and seed coats. One cDNA library each was constructed from its outer stem tissue and inner stem tissue. They comprised a total of 27,752 expressed sequence tags (ESTs) representing 10,520 unigenes made up of 4,302 contigs and 6,218 singletons. Homologues of genes coding for rubber particle membrane proteins that participate in the synthesis of high-molecular poly-isoprene in latex were isolated, as well as those encoding known major latex proteins (MLPs). MLPs extensively shared ESTs, indicating their abundant expression during trans-polyisoprene rubber biosynthesis. The six mevalonate pathway genes which are implicated in the synthesis of isopentenyl diphosphate (IPP), a starting material of poly-isoprene biosynthesis, were isolated, and their role in IPP biosynthesis was confirmed by functional complementation of suitable yeast mutants. Genes encoding five full-length trans-isoprenyl diphosphate synthases were also isolated, and two among those synthesized farnesyl diphosphate from IPP and dimethylallyl diphosphate, an assumed intermediate of rubber biosynthesis. This study should provide a valuable resource for further studies of rubber synthesis in E. ulmoides.     

Metabolic cross talk between cytosolic and plastidial pathways of isoprenoid biosynthesis: unidirectional transport of intermediates across the chloroplast envelope membrane

In higher plants, two independent pathways are responsible for the biosynthesis of isopentenyl diphosphate and dimethylallyl diphosphate, the central five-carbon precursors of all isoprenoids. The cytosolic pathway, which involves mevalonate (MVA) as a key intermediate, provides the precursor molecules for sterols, ubiquinone, and certain sesquiterpenes, whereas the plastidial MVA-independent pathway is involved in the formation of precursors for the biosynthesis of isoprene, monoterpenes, diterpenes, carotenoids, abscisic acid, and the side chains of chlorophylls, tocopherols, and plastoquinone. Recent experiments provided indirect evidence for the presence of an export system for isoprenoid intermediates from the plastids to the cytosol in Arabidopsis thaliana. Here we report that isolated chloroplasts (from spinach, kale, and Indian mustard), envelope membrane vesicles, and proteoliposomes prepared from the solubilized proteins of envelope membranes (from spinach) are capable of the efficient transport of isopentenyl diphosphate and geranyl diphosphate. Lower rates of transport were observed with the substrates farnesyl diphosphate and dimethylallyl diphosphate, whereas geranylgeranyl diphosphate and mevalonate were not transported with appreciable efficiency. Our data suggest that plastid membranes possess a unidirectional proton symport system for the export of specific isoprenoid intermediates involved in the metabolic cross talk between cytosolic and plastidial pathways of isoprenoid biosynthesis.     

Biosynthesis of Carotenoids in the Chloroplasts of Algae and Higher Plants

Physiological, biochemical, and genetic aspects of carotenoid biosynthesis in the chloroplast membranes of green algae and higher plants are discussed starting from the earliest stages of biosynthesis of key C₅-isoprene units. The latter are synthesized either from acetate (C₂) to mevalonic acid (C₆) or from glucose (C₆) by forming glyceraldehyde 3-phosphate (C₃) and pyruvate decarboxylation product (C₂) through intermediate compounds to isopentenyl diphosphate (C₅). In all organisms, the further carotenoid synthesis from isopentenyl diphosphate and its isomer dimethylallyl diphosphate (C₅) proceeds through their transformation into geranyl diphosphate (C₁₀), farnesyl diphosphate (C₁₅), geranylgeranyl diphosphate (C₂₀) and phytoene (C₄₀). Phytoene desaturation (dehydrogenation) to carotene, neurosporene, and lycopene, and all steps of their cyclization to , and carotenes are discussed in detail. The synthesis of xanthophylls in chloroplasts is presented as the sequential formation of hydroxy-, epoxy- and oxo- groups. Genetic control of biosynthesis, as well as the localization and functional role of carotenoids in the chloroplast membranes of plants and algae are briefly discussed.     

Effects of brassinazole,an inhibitor of brassinosteroid biosynthesis,on light- and dark-grown<Emphasis Type="Italic"> Chlorella vulgaris</Emphasis>

Treatment of cultured Chlorella vulgaris Beijerinck cells with 0.1–10 M brassinazole (Brz2001), an inhibitor of brassinosteroid (BR) biosynthesis, inhibits their growth during the first 48 h of cultivation in the light. This inhibition is prevented by the co-application of BR. This result suggests that the presence of endogenous BRs during the initial steps of the C. vulgaris cell cycle is indispensable for their normal growth in the light. In darkness, a treatment with 10 nM brassinolide (BL) promotes growth through the first 24 h of culture, but during the following 24 h the cells undergo complete stagnation. Treatment of dark-grown cells with either Brz2001 alone, or a mixture of 10 nM BL and 0.1/10 M Brz2001, also stimulates their growth. The effects of treatment with 10 nM BL mixed with 0.1–10 M of a mevalonate-pathway inhibitor (mevinolin), or a non-mevalonate-pathway inhibitor (clomazone), were also investigated. Mevinolin at these concentrations did not inhibit growth of C. vulgaris; however, clomazone did. Addition of BL overcame the inhibition. These results suggest that the mevalonate pathway does not function in C. vulgaris, and that the non-mevalonate pathway for isopentenyl diphosphate biosynthesis is responsible for the synthesis of one of the primary precursors in BR biosynthesis.Abbreviations Brz Brassinazole - BL Brassinolide - BR Brassinosteroid - Clo Clomazone - DMAPP Dimethylallyl diphosphate - IPP Isopentenyl diphosphate - MVA Mevalonic acid - Mev Mevinoline     

Regulation of carotenoid biosynthesis in plants: evidence for a key role of hydroxymethylbutenyl diphosphate reductase in controlling the supply of plastidial isoprenoid precursors

Carotenoids are isoprenoid pigments that function as photoprotectors, precursors of the hormone abscisic acid (ABA), colorants and nutraceuticals. A major problem for the metabolic engineering of high carotenoid levels in plants is the limited supply of their isoprenoid precursor geranylgeranyl diphosphate (GGPP), formed by condensation of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) units usually synthesized by the methylerythritol phosphate (MEP) pathway in plastids. Our earlier work with three of the seven MEP pathway enzymes suggested that the first reaction of the pathway catalyzed by deoxyxylulose 5-phosphate synthase (DXS) is limiting for carotenoid biosynthesis during tomato (Lycopersicon esculentum) fruit ripening. Here we investigate the contribution of the enzyme hydroxymethylbutenyl diphosphate reductase (HDR), which simultaneously synthesizes IPP and DMAPP in the last step of the pathway. A strong upregulation of HDR gene expression was observed in correlation with carotenoid production during both tomato fruit ripening and Arabidopsis thaliana seedling deetiolation. Constitutive overexpression of the tomato cDNA encoding HDR in Arabidopsis did not increase carotenoid levels in etioplasts. By contrast, light-grown transgenic plants showed higher carotenoid levels and an enhanced seed dormancy phenotype suggestive of increased ABA levels. The analysis of double transgenic Arabidopsis plants overproducing both the enzyme taxadiene synthase (which catalyzes the production of the non-native isoprenoid taxadiene from GGPP) and either HDR or DXS showed a twofold stronger effect of HDR in increasing taxadiene levels. Together, the data support a major role for HDR in controlling the production of MEP-derived precursors for plastid isoprenoid biosynthesis.     

Biosynthesis of carotenoids in plastids of plants

This review deals with various aspects of the biosynthesis of carotenoids in chromoplasts and chloroplasts of green algae and higher plants. Two pathways of biosynthesis of the key C5-isoprene units are considered: 1) from acetate via mevalonate (C6) followed by its enzymatic conversions to isopentenyl diphosphate (C5); 2) from glucose via formation of glyceraldehyde-3-phosphate (C3) and pyruvate and their condensation via intermediary products to isopentenyl diphosphate (C5). Subsequent biosynthesis of carotenoids from isopentenyl diphosphate (C5) and dimethylallyl diphosphate (C5) involves a common route including their conversion into geranyl diphosphate (C10), farnesyl diphosphate (C15), geranylgeranyl diphosphate (C20), and synthesis of phytoene (C40). All stages of phytoene desaturation accompanied by formation of acyclic compounds such as zeta-carotene, neurosporene, and lycopene and their cyclization to alpha-, beta-, and epsilon-carotenes are considered in detail. Formation of xanthophylls in chloroplasts and chromoplasts involves sequential oxidations yielding hydroxy, epoxy, and oxo groups. Genetic control of biosynthesis of carotenoids is considered.     

Biosynthesis of anthraquinones in cell cultures of the Rubiaceae

Plants and their derived cell and tissue cultures in the family Rubiaceae accumulate a number of anthraquinones. There are two main biosynthetic pathways leading to anthraquinones in higher plants: the polyketide pathway and the chorismate/o-succinylbenzoic acid pathway. The latter occurs in the Rubiaceae for the biosynthesis of Rubia type anthraquinones. In this pathway, ring A and B of the Rubia type anthraquinones are derived from shikimic acid, -ketoglutarate via o-succinylbenzoate, whereas ring C is derived from isopentenyl diphosphate, a universal building block for all isoprenoids. At present, it is known that isopentenyl diphosphate is formed via the mevalonic acid pathway or the 2-C-methyl-D-erythritol 4-phosphate pathway. Recent findings demonstrate that the 2-C-methyl-D-erythritol 4-phosphate pathway, not the mevalonic acid pathway, is involved in the formation of isopentenyl diphosphate, which constitutes ring C of anthraquinones in the Rubiaceae. This review summarizes the latest results of studies on the biosynthetic pathways, the enzymology and regulation of anthraquinone biosynthesis, as well as aspects of the metabolic engineering. Furthermore, biochemical and molecular approaches in functional genomics, which facilitate elucidation of anthraquinone biosynthetic pathways, are briefly described.     

The fellowship of natural abundance 2H-isotopomers of monoterpenes

Site-specific natural abundance hydrogen isotope ratios have been measured by deuterium-NMR in a wide variety of monoterpenes from numerous kinds of plants grown in different environments. Once the NMR signals have been assigned to the whole sets of isotopomers in the different molecules and schemes of connections to the parent isotopomers in the geranyl diphosphate (GPP) precursor have been defined, a very consistent set of isotopic profiles is evidenced. The results, which are incompatible with the mevalonate pathway, can be satisfactorily interpreted by considering the deoxyxylulose pathway (DOXP), which is now recognized as the usual route for monoterpene biosynthesis in plants. Strong deuterium depletion at ex-site 2 of GPP, accompanied by high isotope ratio values at site ex-6, are consistent with synthesis of GPP from isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) molecules independently produced by the DOXP pathway. However, for a given molecular species, significant differences are observed as a function of the plant source, in particular at site ex-6 of GPP. Thus, monoterpenes from plants with a C3 metabolism are mostly characterized by relatively high values of (D/H)6, whereas C4 plants tend to show much lower values. This behavior may be attributed to more or less significant contributions of GPP resulting from the condensation of IPP with DMAPP produced by isomerization. The isotopic profile therefore enables the role of physiological and environmental factors on the relative importance of the "independent" and "isomerized" model to be estimated. More generally, isotope ratios at individual sites in geraniol can be traced back to the corresponding sites in GPP, then to sites of the IPP and DMAPP building blocks, then to the pyruvate and glyceraldehyde 3-phosphate DOXP active molecules, and finally to the carbohydrate photosynthetic precursor. Furthermore, the methylenic hydrogen atoms, which are enantiotopic in geraniol, become diastereotopic in chiral, and more specially in cyclic, monoterpenes. This provides an isotopic verification for the complete stereochemical chain of affiliation, and a way of estimating enantiomeric purity and whether intermolecular exchanges have taken place.     

Determination of the sites of synthesis of chlorophyll synthesizing enzymes in cell cultures of Nicotiana tabacum

The activity of a sequence of enzymes involved in chlorophyll biosynthesis (δ-aminolevulinic acid synthetase (ALAS), δ-aminolevulinic acid dehydratase, porphobilinogenase and chlorophyllase) was followed during greening of tobacco cell cultures under the influence of chloramphenicol (CAP). The photosynthetic enzymes ribulose diphosphate carboxylase (RuDPCO) and NADP linked glyceraldehyde dehydrogenase (NADP-GDH) were used as markers for penetration and action of the inhibitor. RuCPCO was inhibited at concentrations of CAP which still allowed good chlorophyll accumulation. The enzymes of chlorophyll biosynthesis, the activity of which increased during illumination and CAP treatment, behaved like NADP-GDH which is known to be synthesized in the cytoplasm. The results suggest that synthesis of enzymes of chlorophyll biosynthesis takes place in the cytoplasm. Decreasing light induced increment of ALAS activity caused by CAP may possibly be taken as an indication that things are more complicated with this enzyme.     

Thermoinduction of genes encoding the enzymes of gibberellin biosynthesis and a putative negative regulator of gibberellin signal transduction in<Emphasis Type="Italic"> Eustoma grandiflorum</Emphasis>

Eustoma grandiflorum Shinn requires vernalization for the induction of stem elongation and flowering. To investigate the role of gibberellins (GAs) in vernalization, the expression levels of genes encoding enzymes of GA biosynthesis, copalyl diphosphate synthetase, GA 20-oxidase and GA 3-hydroxylase, were examined using two culitvars that show different responses to vernalization. The three genes were induced in a vernalization- and a cultivar-dependent manner. EgSPY, a putative negative regulator of GA signal transduction, was also induced during the vernalization period. The results suggest that the expression of the genes encoding GAs biosynthesis is regulated by vernalization. We postulate that EgSPY functions as a negative regulator of GA signal transduction during vernalization, inhibiting adventitious shoot elongation during vernalization.Communicated by K.K. Kamo