Structure of 2C-methyl-d-erythritol-2,4-cyclodiphosphate synthase involved in mevalonate-independent biosynthesis of isoprenoids

Isoprenoids are biosynthesized from isopentenyl diphosphate and the isomeric dimethylallyl diphosphate via the mevalonate pathway or a mevalonate-independent pathway that was identified during the last decade. The non-mevalonate pathway is present in many bacteria, some algae and in certain protozoa such as the malaria parasite Plasmodium falciparum and in the plastids of higher plants, but not in mammals and archaea. Therefore, these enzymes have been recognised as promising drug targets. We report the crystal structure of Escherichia coli 2C- methyl-d-erythritol-2,4-cyclodiphosphate synthase (IspF), which converts 4-diphosphocytidyl-2C-methyl-d-erythritol 2-phosphate into 2C-methyl-d-erythritol 2,4-cyclodiphosphate and CMP in a Mg-dependent reaction. The protein forms homotrimers that tightly bind one zinc ion per subunit at the active site, which helps to position the substrate for direct attack of the 2-phosphate group on the beta-phosphate.     

Biosynthesis of salvinorin A proceeds via the deoxyxylulose phosphate pathway

Salvinorin A, a neoclerodane diterpenoid, isolated from the Mexican hallucinogenic plant Salvia divinorum, is a potent kappa-opioid receptor agonist. Its biosynthetic route was studied by NMR and HR-ESI-MS analysis of the products of the incorporation of [1-(13)C]-glucose, [Me-(13)C]-methionine, and [1-(13)C;3,4-(2)H2]-1-deoxy-D-xylulose into its structure. While the use of cuttings and direct-stem injection were unsuccessful, incorporation of (13)C into salvinorin A was achieved using in vitro sterile culture of microshoots. NMR spectroscopic analysis of salvinorin A (2.7 mg) isolated from 200 microshoots grown in the presence of [1-(13)C]-glucose established that this pharmacologically important diterpene is biosynthesized via the 1-deoxy-D-xylulose-5-phosphate pathway, instead of the classic mevalonic acid pathway. This was confirmed further in plants grown in the presence of [1-(13)C;3,4-(2)H2]-1-deoxy-D-xylulose. In addition, analysis of salvinorin A produced by plants grown in the presence of [Me-(13)C]-methionine indicates that methylation of the C-4 carboxyl group is catalyzed by a type III S-adenosyl-L-methionine-dependent O-methyltransferase.     

Codon recognition mechanisms in plant chloroplasts

In chloroplasts, all 61 sense codons are found in chloroplast (cp) DNA sequences coding for proteins. However among the sequenced cp tRNAs or tRNA genes, tRNAs with anticodons complementary to codons CUU/C (Leu), CCU/C (Pro), GCU/C (Ala) and CGC/A/G (Arg) [or CGC/A (Arg) in Marchantia] have not been found. In this paper we show that cp tRNA^Ala(U^*GC), cp tRNA^Pro(U^*GG) and cp tRNA^Arg(ICG) are able to decode the corresponding four-codon family. In the case of leucine codons CUU/C, we show that U:U and U:C wobble mechanisms can operate to allow the reading of these codons by cp tRNA^Leu (UAm⁷G).     

Cooperation of photosystem I with the plastoquinone pool in oxygen reduction in higher plant chloroplasts

The possible functions of a light-induced electron transfer to oxygen in the photosynthetic electron transport chain of higher plant chloroplasts are considered. The thermodynamic preconditions, as well as the experimental data about the participations of ferredoxin, the components of photosystems I and II, and plastoquinone in oxygen reduction are examined. It is concluded that, even in the presence of ferredoxin and ferredoxin + NADP⁺, oxygen reduction is carried out mainly by the membrane-bound carriers of the photosynthetic electron transport chain. The hypothesis is put forward that most superoxides, which are produced by reduction of O₂ molecules by the intramembrane components of the acceptor side of photosystem I, are reduced within the membrane by the plastohydroquinone molecules to the hydrogen peroxide. It is assumed that the H₂O₂ molecules that originate as the result of this process serve for signaling about the redox state of the plastoquinone pool. Published in Russian in Biokhimiya, 2008, Vol. 73, No. 1, pp. 137–144.     

Biosynthesis of anthraquinones in cell cultures of Cinchona 'Robusta' proceeds via the methylerythritol 4-phosphate pathway.

Robustaquinone B was found as a major anthraquinone in cell cultures of Cinchona 'Robusta' after treatment with a fungal elicitor. Anthraquinones in Cinchona are considered to be of the Rubia type, i.e. rings A and B are derived from chorismate and alpha-ketoglutarate, whereas ring C is formed from isopentenyl diphosphate (IPP). To determine the origin of IPP, either formed via the mevalonic acid pathway or the 2-C-methyl-D-erythritol 4-phosphate pathway, the incorporation of [1-13C]glucose into robustaquinone B was studied. The 13C labeling of robustaquinone B was analyzed by one- and two-dimensional NMR spectroscopy and the labeling pattern was compared with the hypothetical labeling patterns obtained via the different biosynthetic pathways. The results clearly show that the IPP, constituting the ring C of robustaquinone B, is biosynthesized via the 2-C-methyl-D-erythritol 4-phosphate pathway. Moreover, the data also confirm that rings A and B of robustaquinone B are formed from chorismate and alpha-ketoglutarate via o-succinylbenzoate.     

Production of a recombinant bacterial lipoprotein in higher plant chloroplasts

Little is known about the potential of plastids to accomplish post-translational modifications of foreign proteins. In the present study we generated transplastomic tobacco plants that accumulate the outer surface lipoprotein A (OspA)-the basic constituent of the first generation monovalent human vaccine against Lyme disease. The recombinant OspA exhibits a lipid modification typical for bacteria and induced protective antibodies in mice, demonstrating that functionally active bacterial lipoproteins can be processed in plants.     

The redox potentials of the b-type cytochromes of higher plant chloroplasts

1. In fresh chloroplasts, three b-type cytochromes exist. These are b-559_HP (λ_max, 559 nm; E_m at pH 7, +370 mV; pH-independent E_m), b-559_LP (λ_max, 559 nm; E_m at pH 7, +20 mV; pH-independent E_m) and b-563 (λ_max, 563 nm; E_m at pH 7, ?110 mV; pH-independent E_m). b-559_HP may be converted to a lower potential form (λ_max, 559 nm; E_m at pH 7, +110 mV; pH-independent E_m).2. In catalytically active b-f particle preparations, three cytochromes exist. These are cytochrome f (λ_max, 554 nm; E_m at pH 7, +375 mV, pK on oxidised cytochrome at pH 9), b-563 (λ_max, 563 nm; E_m at pH 7, ?90 mV, small pH-dependence of E_m) and a b-559 species (λ_max, 559 nm, E_m at pH 7, +85 mV; pH-independent E_m).3. A positive method of demonstration and estimation of b-559_LP in fresh chloroplasts is described which involves the use of menadiol as a selective reductant of b-559_LP.     

Membrane polypeptides of some higher plant chloroplasts

Sodium dodecylsulfate-polyacrylamide gel electrophoresis of membrane polypeptides of the mesophyll cell chloroplasts of barley, pea, and maize show similar profiles, with the polypeptides falling into two major groups: those associated with a membrane fraction enriched in Photosystem I (called Group I polypeptides) and those associated with a membrane fraction enriched in Photosystem II (called Group II polypeptides a, b, and c). In contrast to these profiles, the polypeptides from the extensively unstacked membranes of chloroplasts from the chlorophyll-deficient mutant strains of barley and pea as well as those obtained from the agranal bundle sheath cell chloroplasts of maize are deficient in the Group II polypeptides b and c. It is proposed that these polypeptides are required for membrane stacking in higher plant chloroplasts.These Group II polypeptides b and c are not required for Photosystem II activity since both the barley and pea mutant chloroplasts and the maize bundle sheath chloroplasts possess Photosystem II activities.     

Biosynthesis of acyclic and cyclic carotenoids in higher plants and the control by phytochrome

Radish plants ( Raphanus sativus L. cv. Saxa treib) were grown in the presence of three different herbicides interfering with the biosynthesis of cyclic carotenoids. The herbicides caused an accumulation of acyclic biosynthetic intermediates. Plants were then irradiated using four different light programs in order to gain more insight into the first steps of carotenoid biosynthesis and their control by light and phytochrome. Plants grown in the dark in the presence of SAN 6706 or aminotriazole accumulated the acyclic intermediate phytoene, and those treated with J 852, the intermediates phytoene, phytofluene and zeta-carotene. In herbicide-treated plants short time irradiation with red light enhanced the formation of phytoene, phytofluene, zeta-carotene or lycopene, consistent with an effect of phytochrome on the early steps of carotenoid biosynthesis. Biosynthesis of cyclic carotenoids was also enhanced by red light in the untreated controls. In amitrole-treated plants formation of β-carotene, but not that of xanthophylls was stimulated by red light. In many cases neither the red light-induced biosynthesis of cyclic carotenoids nor the formation of acyclic intermediates could be prevented by a subsequent irradiation with far-red light. Similar enhancement as with red light was also obtained after treatment with far-red light only. Presented data may be taken as evidence that the biosynthesis and dehydrogenation of phytoene and the cyclization of lycopene are activated by a low threshold of active phytochrome. This may be further supported by the observation that far-red light itself stimulated carotenoid biosynthesis.     

Immunogold localization of phytoene desaturase in higher plant chloroplasts

In situ location of phytoene desaturase, a key enzyme in the carotenoid biosynthesis pathway, has been investigated in chloroplasts from higher plants. For this purpose, an antiserum has been raised against the phytoene desaturase from the cyanobacterium Synechococcus PCC 7942 overexpressed in E. coli . The specifity of this antiserum was demonstrated by inhibition of the enzymatic desaturation reaction in vitro. The antiserum was further purified and immunoabsorbed with E. coli proteins. The resulting IgG-fraction was tested by western blotting against membrane proteins from chloroplasts of tobacco ( Nicotiana tabacum L. cv. Samsun) and spinach ( Spinacia oleracea L. cv. Atlanta). Apparent molecular masses of immunoreactive proteins were 62 and 64 kDa. A western blot of different membrane fractions of spinach chloroplasts (inner and outer envelopes, and thylakoids) indicated a localization of the phytoene desaturase in thylakoids. A post embedding immunogold microscopy procedure was employed. In these experiments the main labelling (79%) was associated with thylakoid membranes of tobacco chloroplasts. Of the counted colloidal gold particles, 16% were found in the stroma. Only 5% were detected in the envelope membranes. These results give clear evidence that at least the majority of phytoene desaturase molecules is localized within thylakoid membranes of higher plant chloroplasts and that the presence of the enzyme in the envelope is of minor significance.     

Biosynthesis of beta-sitosterol and stigmasterol in Croton sublyratus proceeds via a mixed origin of isoprene units

A green callus culture of Croton sublyratus Kurz established from the leaf explants appeared to actively synthesize two well-known phytosterols, beta-sitosterol and stigmasterol. The phytosterol biosynthesis was highly active during the linear phase of the culture. Feeding of [1-13C]glucose into the callus culture at this growth phase showed that the label from glucose was highly incorporated into both phytosterols. Isolation of the labeled products followed by 13C NMR analysis revealed that the phytosterols had their 13C-labeling patterns consistent with the acquisition of isoprene units via both the mevalonate pathway and the deoxyxylulose pathway with relatively equal contribution. Since the biosynthesis of phytosterol has so far been reported to be mainly from the classical mevalonate pathway, this study provides a new evidence on the biosynthesis of phytosterols via the novel deoxyxylulose pathway.     

高等植物叶绿体RNA编辑研究进展

RNA编辑普遍存在于陆生植物中,在高等植物叶绿体中以C→U的替换为主,可能是叶绿体产生功能蛋白的重要方式。近年来,使用体外分析、叶绿体转化和紫外交联等技术,使叶绿体RNA编辑机制的研究取得较大进展。本文对这些新的进展进行了概述,并对高等植物叶绿体RNA编辑研究中有待解决的问题进行了展望。     

Isoleucine biosynthesis in Leptospira interrogans serotype lai strain 56601 proceeds via a threonine-independent pathway

Three leuA-like protein-coding sequences were identified in Leptospira interrogans. One of these, the cimA gene, was shown to encode citramalate synthase (EC 4.1.3.-). The other two encoded alpha-isopropylmalate synthase (EC 4.1.3.12). Expressed in Escherichia coli, the citramalate synthase was purified and characterized. Although its activity was relatively low, it was strictly specific for pyruvate as the keto acid substrate. Unlike the citramalate synthase of the thermophile Methanococcus jannaschii, the L. interrogans enzyme is temperature sensitive but exhibits a much lower K(m) (0.04 mM) for pyruvate. The reaction product was characterized as (R)-citramalate, and the proposed beta-methyl-d-malate pathway was further confirmed by demonstrating that citraconate was the substrate for the following reaction. This alternative pathway for isoleucine biosynthesis from pyruvate was analyzed both in vitro by assays of leptospiral isopropylmalate isomerase (EC 4.2.1.33) and beta-isopropylmalate dehydrogenase (EC 1.1.1.85) in E. coli extracts bearing the corresponding clones and in vivo by complementation of E. coli ilvA, leuC/D, and leuB mutants. Thus, the existence of a leucine-like pathway for isoleucine biosynthesis in L. interrogans under physiological conditions was unequivocally proven. Significant variations in either the enzymatic activities or mRNA levels of the cimA and leuA genes were detected in L. interrogans grown on minimal medium supplemented with different levels of the corresponding amino acids or in cells grown on serum-containing rich medium. The similarity of this metabolic pathway in leptospires and archaea is consistent with the evolutionarily primitive status of the eubacterial spirochetes.     

Polyunsaturated fatty acyl residues of galactolipids are involved in the control of bilayer/non-bilayer lipid transitions in higher plant chloroplasts

Total polar lipid extracts of chloroplasts isolated from broad beans (Vicia faba) tend to form non-bilayer structures when dispersed in dilute salt solutions. Monoglactosyldiacylglycerol is shown to play a dominant role in this process. The tendency of this lipid to form non-bilayer structures when dispersed alone in water was found to depend upon the degree of unsaturation of its associated fatty acyl chains. Highly unsaturated lipids (average number of double bonds per lipid molecule greater than about 5.0) form inverted hexagonal (Hex_II) structures in water at 20°C, whilst more saturated lipids (average number of double bonds per lipid molecule less than about 4.5) form lamellar sheets. Wide-angle X-ray diffraction and differential scanning calorimetry measurements indicate that these lamellae consist of gel-phase lipid that can adopt either of two structures depending on the thermal history of the sample. Freeze-fracture studies performed on total polar lipid extracts that have been hydrogenated using Adams' catalyst, and reconstituted extracts in which monogalactosyldiacylglycerol has been selectively hydrogenated, show that the degree of unsaturation of this lipid is a key factor in determining whether or not non-bilayer structures are formed in such extracts. Increasing the extent of saturation of the acyl residues of monogalactosyldiacylglycerol reduces the tendency to form non-bilayer structures. Similar effects are observed on lowering the temperature of the dispersions. Fluorescence polarisation measurements using 1,6-diphenyl-1,3,5-hexatriene indicate that the disappearance of non-bilayer structures is accompanied by a marked decrease in the fluidity of the lipid matrix. The possible significance of these observations is discussed in terms of the thermal adaptation and chilling sensitivity of plant membranes.     

Isolation of biochemically active chloroplasts from chlamydomonas

Chloroplasts from the cell wall mutant cw-15-2 of Chlamydomonas reinhardii were isolated by disruption of the cells in the Yeda press and fractionation through step gradients of Percoll. The resulting chloroplast fraction contained 80–85% intact chloroplasts. Electron micrographs of thin sections of the chloroplast fraction showed some cytoplasmic impurities, although almost no cytoplasmic ribosomes were detected by analysis of the ribosomal subunits.The isolated chloroplasts are active in photosynthetic O₂-evolution and CO₂-fixation, with the highest rates obtained in the presence of ATP.The chloroplast fraction also showed high rates of light-dependent in organello protein synthesis, with labelling of discrete chloroplast proteins known to be synthesized in the chloroplasts.     

Photosystem I reaction centers fromChlamydomonas and higher plant chloroplasts

A photosystem I reaction center has been isolated fromChlamydomonas chloroplasts and compared with the photosystem I reaction center from higher plants. While the higher plant reaction center is active in cytochrome 552 photooxidation, theChlamydomonas preparation was not active unless salts were included in the assay medium or the pH was lowered to 5. Subunit III-depleted photosystem I reaction center from higher plants is also inactive in cytochrome 552 photooxidation in the absence of salts. As with theChlamydomonas reaction center, salts induced its activity. Subunit I of the photosystem I reaction center has tentatively been identified as the binding site of cytochrome 552.