DXS Genes Research Articles

Replicon‐free and markerless methods for genomic insertion of DNAs in phage attachment sites and controlled expression of chromosomal genes in Escherichia coli

Genetic manipulation of cells for desired traits is the most appreciable strategy implemented in the field of bioengineering. However, this approach closely relies on the use of plasmids and is commonly afflicted by the potential problem of plasmid instability and safety caution. Meanwhile, it may also lead to the spread of antibiotic-resistant markers with replicons of plasmids to the environment. However, this issue has long been neglected. In this study, we have addressed these subjects by developing replicon-free and markerless methods for chromosomal insertion of genes and controlled expression of genomic genes in Escherichia coli. For the former application, the integration vectors of conditional replication were incorporated with the prophage attachment site and duplicated FRT sites. Their utility was illustrated by site-specific insertion of target genes, the endogenous dxs gene and three heterologous genes consisting of gps, crtI, and crtB, fused to T7 promoter into E. coli genome. For the latter application, the template vectors for promoter replacement were constructed to carry a DNA cassette containing the T7 promoter linked to a selective marker flanked with the FRT site. Subsequently, it was illustrated by replacement of the native promoter of chromosomal pckA by the T7 promoter. Finally, with the aid of FLP recombinase supplied from a helper plasmid, the regions containing replicon and/or selective markers in inserted DNAs were eliminated from integrants for both approaches. As a consequence, the expression of these five genes was subject to control by one response regulator, T7 RNA polymerase, in a regulon way, resulting in a high and stable production of lycopene in the cell. This result indicates the promise of developed methods for genome engineering in E. coli.

Identification and characterization of class 1 DXS gene encoding 1-deoxy-d-xylulose-5-phosphate synthase, the first committed enzyme of the MEP pathway from soybean

1-Deoxy-D-xylulose-5-phosphate synthase (DXS) catalyses the first committed step of the 2C-methyl-D-erythritol-4-phosphate (MEP) pathway, which is an alternative isoprenoids biosynthetic route that has been recently discovered. In this work, a DXS1-like cDNA (GmDXS1) was isolated from soybean. The full-length cDNA of GmDXS1 encoded 708 amino acid residues with a predicted molecular mass of 76.4 KD. Sequence alignment showed that GmDXS1 had high homology to known DXS proteins from other plant species and contained the conserved N-terminal plastid transit peptide, the N-terminal thiamine binding domain and pyridine binding DRAG domain. Phylogenetic analysis indicated that GmDXS1 belonged to the plant DXS1 cluster. Southern blot analysis indicated that a single copy of GmDXS1 gene existed in soybean genome. Tissue expression analysis revealed that GmDXS1 expressed in all photosynthetic tissues except pod walls and roots. Green fluorescence analysis with the fusion protein 35S:GmDXS1:GFP suggested that GmDXS1 was localized in plastid. The relatively higher photosynthetic pigment content in transgenic tobacco leaves compared to the control implied that GmDXS1 catalyzed the first potential regulatory step in photosynthetic pigment biosynthesis via the MEP pathway.

Functional identification and differential expression of 1-deoxy-d-xylulose 5-phosphate synthase in induced terpenoid resin formation of Norway spruce (Picea abies)

Conifers produce terpenoid-based oleoresins as constitutive and inducible defenses against herbivores and pathogens. Much information is available about the genes and enzymes of the late steps of oleoresin terpenoid biosynthesis in conifers, but almost nothing is known about the early steps which proceed via the methylerythritol phosphate (MEP) pathway. Here we report the cDNA cloning and functional identification of three Norway spruce (Picea abies) genes encoding 1-deoxy-D-xylulose 5-phosphate synthase (DXS), which catalyzes the first step of the MEP pathway, and their differential expression in the stems of young saplings. Among them are representatives of both types of plant DXS genes. A single type I DXS gene is constitutively expressed in bark tissue and not affected by wounding or fungal application. In contrast, two distinct type II DXS genes, PaDXS2A and PaDXS2B, showed increased transcript abundance after these treatments as did two other genes of the MEP pathway tested, 1-deoxy-D-xylulose 5-phosphate reductoisomerase (DXR) and 4-hydroxyl 3-methylbutenyl diphosphate reductase (HDR). We also measured gene expression in a Norway spruce cell suspension culture system that, like intact trees, accumulates monoterpenes after treatment with methyl jasmonate. These cell cultures were characterized by an up-regulation of monoterpene synthase gene transcripts and enzyme activity after elicitor treatment, as well as induced formation of octadecanoids, including jasmonic acid and 12-oxophytodienoic acid. Among the Type II DXS genes in cell cultures, PaDXS2A was induced by treatment with chitosan, methyl salicylate, and Ceratocystis polonica (a bark beetle-associated, blue-staining fungal pathogen of Norway spruce). However, PaDXS2B was induced by treatment with methyl jasmonate and chitosan, but was not affected by methyl salicylate or C. polonica. Our results suggest distinct functions of the three DXS genes in primary and defensive terpenoid metabolism in Norway spruce.

Cloning and characterization of the dxs gene, encoding 1-deoxy-d-xylulose 5-phosphate synthase from Agrobacterium tumefaciens, and its overexpression in Agrobacterium tumefaciens

A newly isolated gene dxs11 from Agrobacterium tumefaciens (KCCM 10413), an organism with potential for the industrial production of ubiquinone-10 (UbiQ(10)), encoding a 1-deoxy-d-xylulose 5-phosphate synthase (Dxs), was cloned in Escherichia coli and its nucleotide sequence was determined. DNA sequence analysis revealed an open reading frame of 1920bp, capable of encoding a polypeptide of 640 amino acids residues with a calculated isoelectric point of pH 5.63 and a molecular mass of 68,054Da. The homodimeric enzyme was overexpressed in E. coli and purified as an active soluble form. The enzyme required thiamine diphosphate and a divalent metal ion, either Mg(2+) or Mn(2+), for enzymatic activity. The enzyme had an optimal pH and temperature of 8.0 and 37 degrees C, respectively, with a k(cat) of 26.8s(-1) and a k(cat)/K(m) of 0.67 and 1.17s(-1)M(-1) for pyruvate and d-glyceraldehyde 3-phosphate, respectively. A. tumefaciens Dxs showed a comparable catalytic efficiency to other Dxs proteins. The dxs11 gene was transformed into A. tumefaciens KCCM 10413, and the resulting recombinant, A. tumefaciens pGX11, showed higher UbiQ(10) production (502.4mg/l) and content (8.3mg/gDCW) than A. tumefaciens KCCM 10413, by 21.9 and 23.9%, respectively. This work describes Dxs from A. tumefaciens, an organism with the potential for industrial UbiQ(10) production, and the first metabolic engineering study with the non-mevalonate pathway enzyme in A. tumefaciens.

Amplification of 1-deoxy-d-xyluose 5-phosphate (DXP) synthase level increases coenzyme Q10 production in recombinant Escherichia coli

For the enhancement of coenzyme Q(10) (CoQ(10)) production, 1-deoxy-D-xylulose 5-phosphate (DXP) synthase of Pseudomonas aeruginosa was constitutively coexpressed in a recombinant Escherichia coli strain, which harbors the ddsA gene from Gluconobacter suboxydans encoding decaprenyl diphosphate synthase. It was found that the expression of the ddsA gene caused depletion of the isopentenyl diphosphate (IPP) pool in E. coli. Amplification of DXP synthase level by installing P. aeruginosa DXP synthase restored the diminished IPP pool and concomitantly resulted in approximately a twofold increase in relative content and productivity of CoQ(10). Maximum CoQ(10) concentration of 46.1 mg l(-1) was achieved from glucose-limited fed-batch cultivation of the recombinant E. coli strain simultaneously harboring the ddsA and dxs genes.

Molecular cloning and expression of a cDNA encoding 1-deoxy- d-xylulose-5-phosphate synthase from oil palm Elaeis guineensis Jacq.

In higher plants, there are two pathways leading to the formation of isoprenoids: the acetate/mevalonate (MVA) pathway and the recently discovered 2C-methyl- d-erythritol-4-phosphate (MEP) pathway. The initial step on the MEP pathway is the condensation of pyruvate and glyceraldehyde-3-phosphate yielding 1-deoxy- d-xylulose-5-phosphate (DXP). The reaction is catalyzed by 1-deoxy- d-xylulose-5-phosphate synthase (DXS), and is encoded by the dxs gene. In this study, parts of dxs have been cloned from young leaves and mesocarp of oil palm ( Elaeis guineensis Jacq., Tenera) The surprising results show that there are at least two dxs genes encoding DXS in different organs of oil palm, dxs1 in leaves and dxs2 in fruits. Cloning of full-length cDNA encoding dxs1 by the RLM-RACE (RNA ligase-mediated rapid amplification of 5 ′ and 3 ′ cDNA ends) method demonstrated that the cDNA contained an open reading frame of 2301 bp encoding a deduced peptide of 707 amino acid residues with a predicted molecular mass of 76.4 kDa and isoelectric point of 7.0. Expression of dxs2 and dxr transcript levels in oil palm fruits from each developmental stage were analyzed by a semiquantitative RT-PCR method. The level of dxs2 transcripts increases with the time after fertilization and reaches its maximum after 18 weeks while the expression of dxr is unchanged. The pattern of dxs2 transcripts appears to correlate with β-carotene accumulation during oil palm fruit ripening thus supports the assumed role of the dxs gene in carotenoid biosynthesis by the MEP pathway.

Phytochrome Regulation of Carotenoid Biosynthesis during Ripening of Tomato Fruit

The accumulation of carotenoids such as lycopene and beta-carotene greatly influences the quality of ripe tomato (Lycopersicon esculentum) fruit because cellular levels of these compounds determine the intensity of red color. As well, lycopene has anti-cancer properties and beta-carotene is a Vitamin A precursor. Recent work has demonstrated phytochrome regulation of the carotenoid pathway but the mechanism is not completely understood. This work investigates phytochrome regulation of 1-deoxy-D-xylulose 5-phosphate synthase (DXS) and phytoene synthase (PSY), two key enzymes of carotenogenesis. A simple procedure for the assay of PSY from crude pericarp extracts was developed and mRNA levels of DXS and PSY1 genes were measured by relative RT-PCR. Discs from mature green tomatoes were ripened in total darkness, or in darkness interrupted by brief daily treatments of red light, or red light followed by far red light. After ten days of incubation, lycopene levels of red light-treated discs had reached ≈12 mg/100 g fresh weight; nearly a 50% increase over discs ripened in total darkness. This increase was not observed in discs treated with red light followed by far red light, demonstrating the red/far red reversibility (and thus phytochrome control) of carotenoid accumulation. Similar patterns of phytochrome control are observed for PSY activity but not for DXS and PSY1 transcript levels, suggesting the mechanism of control may be at the level of post-translational modification of PSY. Potential applications of this regulation of carotenoid accumulation will be discussed.

High-performance liquid chromatography assay for 1-deoxy- d-xylulose 5-phosphate synthase activity using fluorescence detection

A high-performance liquid chromatography assay for activity of 1-deoxy- d-xylulose 5-phosphate synthase, an early enzyme in the recently discovered 2-C-methyl- d-erythritol-4-phosphate pathway, was developed. In this assay, the enzymatic product 1-deoxy- d-xylulose was first derivatized with a fluorescent reagent 2-anthranilic acid, followed by separation using HPLC on a Nova-Pak phenyl column with a mobile phase containing CH 3CN–water–1-butylamine–tetrahydrofuran–H 3PO 4 (2:97:0.125:0.5:0.25, v/v). The eluate was monitored by fluorescence detection at an excitation wavelength of 320 nm and an emission wavelength of 425 nm for quantitation of the fluorescent derivative. A linear response was obtained between 5 and 200 ng of 1-deoxy- d-xylulose. This assay was successfully applied to measure the 1-deoxy- d-xylulose 5-phosphate synthase activity in a recombinant E. coli overexpressing dxs gene. It demonstrated that this assay is simple, sensitive and selective compared to the methods used at present.

Two distantly related genes encoding 1-deoxy-d-xylulose 5-phosphate synthases: differential regulation in shoots and apocarotenoid-accumulating mycorrhizal roots.

Isopentenyl diphosphate, the universal precursor of isoprenoids, is synthesized by two separate routes, one in the cytosol and the other in plastids. The initial step of the plastidial pathway is catalysed by 1-deoxy-d-xylulose 5-phosphate synthase (DXS), which was previously thought to be encoded by a single-copy gene. We have identified two distinct classes of DXS-like cDNAs from the model legume Medicago truncatula. The deduced mature MtDXS1 and MtDXS2 proteins, excluding the predicted plastid-targeting peptides, are similar in size (72.7 and 71.2 kDa) yet share only 70% identity in their amino acid sequences, and both encode functional DXS proteins as shown by heterologous expression in Escherichia coli. Available DXS sequences from other plants can easily be assigned to either class 1 or class 2. Partial sequences of multiple DXS genes in a single genome may be found in the databases of several monocot and dicot plants. Blot analyses of RNA from M. truncatula, maize, tomato and tobacco demonstrate preferential expression of DXS1 genes in many developing plant tissues except roots. By contrast, DXS2 transcript levels are low in most tissues but are strongly stimulated in roots upon colonization by mycorrhizal fungi, correlated with accumulation of carotenoids and apocarotenoids. Monoterpene-synthesizing gland cells of leaf trichomes appear to be another site of DXS2 gene activity. The potential importance of DXS1 in many housekeeping functions and a still hypothetical role of DXS2 in the biosynthesis of secondary isoprenoids is discussed.

Growth-phase dependent expression of the mevalonate pathway in a terpenoid antibiotic-producing Streptomyces strain.

Streptomyces griseolosporeus MF730-N6, a terpenoid antibiotic-terpentecin (Tp) producer, has both the nonmevalonate and mevalonate pathways for the formation of IPP. The Tp biosynthetic gene (ter) and the mevalonate pathway gene cluster (mev) including an HMG-CoA reductase gene (hmgr) had previously been cloned from strain MF730-N6. In this study, two distinct dxs genes (dxs 1 and dxs 2) and a dxr gene, which encode DXP synthases and DXP reductoisomerase, and participate in the initial and the second step of the nonmevalonate pathway, respectively, were cloned. These gene products were expressed in E. coli and confirmed to have the expected activities. The dxs 1, dxs 2, dxr, mev, and ter genes were used for Northern blot and primer extension analyses to examine temporal expression of these genes together with a gap gene coding for GAP dehydrogenase, which was also cloned in this study and used as an internal control. Transcripts of the dxs 1, dxs 2, dxr, and gap genes were detected throughout the cultivation. On the other hand, messages of the mev and ter genes were not detected at early growth phase but appeared when Tp production started. These results suggested that the nonmevalonate pathway and the mevalonate pathway were mainly used for the primary metabolism and the secondary metabolism, respectively, and that both of the two dxs genes were actually transcribed in this strain.

Carotenoid biosynthesis during tomato fruit development: regulatory role of 1-deoxy-D-xylulose 5-phosphate synthase.

Plant isoprenoids represent a heterogeneous group of compounds which play essential roles not only in growth and development, but also in the interaction of plants with their environment. Higher plants contain two pathways for the biosynthesis of isoprenoids: the mevalonate pathway, located in the cytosol/endoplasmic reticulum, and the recently discovered mevalonate-independent pathway (Rohmer pathway), located in the plastids. In order to evaluate the function of the Rohmer pathway in the regulation of the synthesis of plastidial isoprenoids, we have isolated a tomato cDNA encoding 1-deoxy-D-xylulose 5-phosphate synthase (DXS), the first enzyme of the pathway. We demonstrate in vivo activity and plastid targeting of plant DXS. Expression analysis of the tomato DXS gene indicates developmental and organ-specific regulation of mRNA accumulation and a strong correlation with carotenoid synthesis during fruit development. 1-Deoxy-D-xylulose feeding experiments, together with expression analysis of DXS and PSY1 (encoding the fruit-specific isoform of phytoene synthase) in wild-type and yellow flesh mutant fruits, indicate that DXS catalyses the first potentially regulatory step in carotenoid biosynthesis during early fruit ripening. Our results change the current view that PSY1 is the only regulatory enzyme in tomato fruit carotenogenesis, and point towards a coordinated role of both DXS and PSY1 in the control of fruit carotenoid synthesis.