geranyl diphosphate  (Echelon Biosciences)

Journal: iScience

Article Title: Transcriptome-informed identification and characterization of Planococcus citri cis - and trans -isoprenyl diphosphate synthase genes

doi: 10.1016/j.isci.2024.109441

Figure Lengend Snippet:

Article Snippet: Geranyl diphosphate (GPP) , Echelon Biosciences , I-0100.

Techniques: Virus, Recombinant, Expressing, Plasmid Preparation, Software

Journal: iScience

Article Title: Transcriptome-informed identification and characterization of Planococcus citri cis - and trans -isoprenyl diphosphate synthase genes

doi: 10.1016/j.isci.2024.109441

Figure Lengend Snippet: Phylogenetic tree of P. citri trans -IDS candidates and characterized trans -IDS sequences from Hemiptera species The predicted functions are shown in colored rectangles (DPPS, decaprenyl diphosphate synthase; GGPPS, geranylgeranyl diphosphate synthase; FPPS, farnesyl diphosphate synthase). The maximum-likelihood tree is drawn to scale, with branch lengths measured in the number of substitutions per site (scale on the bottom left). Bootstrap values (1,000 replicates) are shown next to nodes. We included all P. citri trans -IDS candidates, except for trans IDS17, a predicted ubiquitin thioesterase, and examples of IDS sequences from Hemiptera species, which were characterized in vitro . The latter include sequences from aphids ( Megoura viciae , , Aphis gossypii , Myzus persicae , and Acyrthosiphon pisum ) and from shield bugs ( Halyomorpha halys , Nezara viridula , and Murgantia histrionica . See Figure S9 for the alignment of P. citri trans -IDS sequences included in the phylogenetic tree.

Article Snippet: Isopentenyl, dimethylallyl, and geranyl diphosphate (IPP, DMAPP, and GPP) were purchased as tri-ammonium salts from Echelon Biosciences (Salt Lake City, UT, USA).

Techniques: In Vitro

Journal: iScience

Article Title: Transcriptome-informed identification and characterization of Planococcus citri cis - and trans -isoprenyl diphosphate synthase genes

doi: 10.1016/j.isci.2024.109441

Figure Lengend Snippet: In vitro activity of P. citri IDS sequences expressed in E. coli Measured enzymatic activity for production of C10 and C15 prenyl diphosphates (A), chromatogram of standard geraniol (peak 1A in upper panel) and trans IDS5 product (peak 1B in lower panel) (B), and schematic representation of confirmed coupling reactions performed by P. citri trans -IDS candidates (C). Trans IDS5, trans ID11, trans IDS2, and trans IDS17 produced C10 geranyl diphosphate (GPP) and C15 farnesyl pyrophosphate (FPP); trans IDS3 produced C10 GPP and cis -isogeranyl diphosphate and two C15 FPP isomers. (A) Activity for production of C10 prenyl diphosphates (light blue bars) and activity for production of C15 prenyl diphosphates (dark blue bars). Height of the bars represents the mean of three separate measurements, plotted as block dots. Raw data are available in Table S5 . Note the y axis break due to the much higher activity of trans IDS5. We did not detect any C10 or C15 products with other tested candidates ( Table 1 ). Chromatograms in (B) are also shown in Figure S16 . MS spectra of highlighted peaks are given in Figure S17 . Chromatograms and MS spectra of products obtained with other candidates are available in Figures S16–S27 . In (C), dimethylallyl diphosphate (DMAPP) can be joined to its isomer isopentenyl diphosphate (IPP) to form regular geranyl and iso-geranyl diphosphates (GPP and iso-GPP) and isomers of farnesyl diphosphate (FPP). FPP is a precursor for juvenile hormone biosynthesis, as denoted by the dashed arrow. Alternatively, two DMAPP units can be assembled into irregular lavandulyl diphosphate (LPP) and maconellyl diphosphate (MPP). The structure of planococcyl acetate (PAc), the sex pheromone of P. citri , is shown in brackets and is presumed to result from the coupling of two DMAPP units as well.

Article Snippet: Isopentenyl, dimethylallyl, and geranyl diphosphate (IPP, DMAPP, and GPP) were purchased as tri-ammonium salts from Echelon Biosciences (Salt Lake City, UT, USA).

Techniques: In Vitro, Activity Assay, Produced, Blocking Assay

Journal: iScience

Article Title: Transcriptome-informed identification and characterization of Planococcus citri cis - and trans -isoprenyl diphosphate synthase genes

doi: 10.1016/j.isci.2024.109441

Figure Lengend Snippet: Mutagenesis of trans IDS5 active site residues (A) Activity of trans IDS5 and its mutants expressed in E. coli. Activity for the production of C10 geranyl diphosphate (GPP, light blue bars) and activity for the production of C15 farnesyl diphosphate (FPP, dark blue bars) are plotted. Height of the bars represents the mean of three separate measurements, plotted as black dots. Raw data are available in Table S5 . (B) Mutated amino acids and their position in the active site, based on a computational model of active center of trans IDS5 with two bound substrate (IPP) molecules showing the aspartate of the first (D166) and the second (D308, D309, D312) aspartate-rich motifs and lysine 120 (K120). Oxygen atoms in aspartate side chains and in pyrophosphate moieties (PPi) of the substrates are shown in red; the nitrogen atom of lysine side chain is highlighted in blue.

Article Snippet: Isopentenyl, dimethylallyl, and geranyl diphosphate (IPP, DMAPP, and GPP) were purchased as tri-ammonium salts from Echelon Biosciences (Salt Lake City, UT, USA).

Techniques: Mutagenesis, Activity Assay

Journal: iScience

Article Title: Transcriptome-informed identification and characterization of Planococcus citri cis - and trans -isoprenyl diphosphate synthase genes

doi: 10.1016/j.isci.2024.109441

Figure Lengend Snippet:

Article Snippet: Isopentenyl, dimethylallyl, and geranyl diphosphate (IPP, DMAPP, and GPP) were purchased as tri-ammonium salts from Echelon Biosciences (Salt Lake City, UT, USA).

Techniques: Virus, Recombinant, Expressing, Plasmid Preparation, Software

Journal: International Journal of Biological Sciences

Article Title: An apoA-I mimetic peptide increases LCAT activity in mice through increasing HDL concentration

doi:

Figure Lengend Snippet: ABCA1 dependent cholesterol efflux assay. The assay details are described in Materials and Methods. A, ABCA1 expression levels in RAW cells were determined by western blot with anti-mouse ABCA1 antibody. Very low basal expression levels of ABCA1 are dramatically increased by the addition of cAMP. B, apoA-I-stimulated cholesterol efflux from macrophage is ABCA1 level dependent. C, apoA-I and its formulated particles show activity in stimulating cholesterol efflux through the ABCA1 transporter, providing EC 50 values of 101 nM and 103 nM, respectively. D, D-4F and its formulated particles show activity in stimulating cholesterol efflux through the ABCA1 transporter, providing EC 50 values of 2.2 μM and 2.8 μM, respectively. F, both size and discoidal shape of D-4F particles made with Dipalmitoylphosphatidylcholine ( DPPC ) (D4F:DPPC = 1:10) were confirmed by electron microscope (Magnification 45000, disk size; 6 x 12 nm).

Article Snippet: Goat anti-mouse apoA-I polyclonal antibody was from Rockland Immunochemicals Inc. (600-101-196; Gilbertsville, PA).

Techniques: Expressing, Western Blot, Activity Assay, Microscopy

Journal: International Journal of Biological Sciences

Article Title: An apoA-I mimetic peptide increases LCAT activity in mice through increasing HDL concentration

doi:

Figure Lengend Snippet: D-4F increases plasma LCAT activity, HDL, and apoA-I in vivo . ApoE-null mice were injected subcutaneously with D-4F peptide at 20 mg/kg once daily for 3 days, and plasma samples were collected at different time points. LCAT activity and HDL concentrations were measured as described in Materials and Methods. A, plasma LCAT activity of apoE-null mouse after D-4F treatment (□ Vehicle, ■ D-4F treated). The plasma samples were collected 24 hours after first (24 h) and third (72 h) dosing. No change of LCAT activity was seen at 24 hours after single dosing while a significant increase of LCAT activity was seen 24 hours after the third dosing ( p = 2x10 -6 ). Results were from two independent experiments. B, correlation between LCAT activity and HDL concentration. LCAT activities of control plasma (●) and 24 hr after third dose with D-4F (▼) were plotted against their HDL concentrations. The goodness-of-fit of linear regression ( r 2 ) is 0.64. C, apoA-I ELISA of apoE-null mouse plasma collected from control group (open bar) and 24 hours after third dose with D-4F (closed bar). Error bars represented the standard division (*: P<0.05, ***: P<0.001).

Article Snippet: Goat anti-mouse apoA-I polyclonal antibody was from Rockland Immunochemicals Inc. (600-101-196; Gilbertsville, PA).

Techniques: Activity Assay, In Vivo, Injection, Concentration Assay, Enzyme-linked Immunosorbent Assay