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Fig. 6 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 6. Characterization of Aa7DR1 as a 7-dehydrocholesterol reductase 1 from A. asphodeloides Bunge.

Fig. 4 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 4. Transcriptional levels of candidate 7-DR genes involved in timosaponin biosynthesis by RT-qPCR. The characters on the X-axis indicate the roots (R), shortening stem (S) and leaves (L). The Y-axis represents the fold change in gene expression. The ubiquitin gene was used as an internal reference.

Fig. 4 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 4. DEG functional enrichment during different growth stages. Pathway functional enrichment of differential expressed genes (DEGs) by using Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Pathways are at the yaxis plot, while rich factor values are at the x-axis. Size of the dots reflect gene number; small dot means 500 genes, big dot means 1000 genes. Darker the color of the dot means the highest the significant value of enrichment (Q-value). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 5. 7-dehydrocholesterol reductase (7-DR) are involved in cholesterol and phytosterol biosynthesis. CAS: cycloartenol synthase; LAS: lansterol synthase; SMT: sterol C-24 methyltransferase; SSR: sterol side chain reductase; Erg1:squalene epoxidase; Erg5: sterol C-22 desaturase; Erg4: C-24 sterol reductase.

Fig. 3 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 3. Content analyses of steroidal saponins (A) and phytosterols in different organs of A. asphodeloides Bunge. Corresponding histograms indicate the difference in concentration among the different organs. Three biological replicates were performed for each sample.

Fig. 6 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 6. Summary differential expressed genes (DEGs) in photosynthesis – antenna proteins pathway (second most enriched pathway) using Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis. The genes at early stationary growth phase were normalized against genes at early exponential growth phase. Green color means down-regulated DEGs; red color means up-regulated DEGs; black color means no DEGs. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 1. Functional annotation of unigenes. Ratio of different species maps on transcripts annotation analysis based on non-redundant (NR) protein databases. Blue color means Monoraphidium neglectum; green color means other species; orange means Porphyra umbilicalis; grey color means Aureococcus anophagefferens; yellow color means Guillardia theta CCMP2712; purple color means Chlamydomonas reinhardtii. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 5. Top DEG pathway enrichment involved during different growth stages. Summary of differential expressed genes (DEGs) identified in photosynthesis pathway (most enriched pathway) of M. gracile SE-MC4 according to Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis. The genes at early stationary growth phase were normalized against genes at early exponential growth phase. Green color means down-regulated DEGs; red color means up-regulated DEGs; black color means no DEGs. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 7 in Transcriptomic investigation of the biochemical function of 7-dehydro- cholesterol reductase 1 from the traditional Chinese medicinal plant Anemarrhena asphodeloides Bunge

Fig. 7. Phylogenetic tree of 7-dehydrocholesterol reductase. Sequences from the following species were represented: A. asphodeloides Bunge (Aa), Arabidopsis thaliana L. (Brassicaceae) (At), Brachypodium distachyon L. (Poaceae) (Bd), Capsicum annuum L. (Solanaceae) (Ca), Chlamydomonas reinhardtii (Cr), Homo sapiens (Hs), Medicago truncatula Gaetn (Leguminosae) (Mt), Nicotiana. Benthamiana Domin (Solanaceae) (Nb), Ostreococcus lucimarinus (Ol), Oryza sativa L. (Poaceae) (Os), Ostreococcus tauri (Ot), Physcomitrella patens (Pp), Sorghum bicolor L. (Poaceae) (Sb), Saccharomyces cerevisiae (Sc), Solanum lycopersicum L. (Solanaceae) (Sl), Solanum melongena L. (Solanaceae) (Sm), Solanum tuberosum L. (Solanaceae) (St), Volvax carteri (Vc), Vitis vinifera L. (Vitaceae) (Vv) and Zea mays L. (Poaceae) (Zm).

Fig. 3 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 3. Differential expressed gene analysis (DEG) of transcriptome. DEG in Volcano plot (log transform of early exponential growth and early stationary growth phases versus inverse log Padj – corrected P-value). Up-regulated DEGs are in red color dots, down-regulated DEGs are in blue dots, while grey dots represent no significant DEGs. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Transcriptome-wide study in the green microalga Messastrum gracile SE-MC4 identifies prominent roles of photosynthetic integral membrane protein genes during exponential growth stage

Fig. 2. Transcriptome expression analysis during different growth stages. (a) Venn diagram for specific treatment genes. Venn diagram constructed based on subset between gene pools in the early exponential and early stationary growth phases of M. gracile SEMC4 cultures. The total number of early exponential growth-specific (EEG-specific) genes (blue subset); early stationary growth-specific (ESG-specific) genes (pink sub set) and regulatory genes (purple sub set) are as indicated. (b) Soft clustering based on time series analysis on expression changes between early exponential growth and early stationary growth phases of M. gracile SE-MC4 cultures. R1, R2 and R3 are the biological replicates of each early exponential (day 1) and early stationary (day 12) growth phase of M. gracile SE-MC4 cultures. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 6 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 6. Multiple sequence alignment for the catalytic domain of V. betonicifolia protein disulfide isomerases, VbPDI1-2 with previously reported PDIs from Rubiaceae (OaPDI) and Violaceae (GbPDI). The active site residues CGHC are highlighted.

Fig. 4 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 4. Vibe cyclotide/acyclotide properties A. Graphical representation of net acidity, basicity and hydrophobicity of cyclotide/acyclotide* from V. betonicifolia, calculated using a peptide property calculation tool, https://www.peptide2.com/N_peptide_hydrophobicity_hydrophilicity.php (Kyte and Doolittle, 1982; Sims, 2010). B. Sequence alignment highlighting physicochemical similarity. Hydrophobic residues are highlighted in yellow, basic in red and acidic in blue. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 3 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 3. Vibe cyclotides identified from small scale extraction of V. betonicifolia. A. Base peak ion (BPI) chromatogram from V. betonicifolia containing deconvoluted masses for (M + H)+ of candidate cyclotides. B. Isotopic mass pattern of native, reduced/alkylated, endoproteinase GluC cleaved cyclotides exemplified by kalata S/ varv A (B), vibe 13 (C) and a new cyclotide present in the extract but absent in the transcriptome (D).

Fig. 2 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 2. Schematic representation of the general organisation of cyclotide precursors and multiple sequence alignment of 28 cyclotide precursor proteins obtained from the de novo transcriptome assembly of V. betonicifolia. A. ER signal domain at the start of each precursor sequence is highlighted in blue where cleavage of the signal domain is predicted to occur between blue and pink residues (Dutton et al., 2004). The precursor is organised with an N-terminal propeptide domain, NTPP (black), N-terminal repeat, NTR (green), mature cyclotide domain (red) and C-terminal propeptide domain, CTPP (purple). An AEP mediated cleavage potentially occurs at the conserved Asn/Asp adjacent to the CTPP of all cyclotide sequences; B. New cyclotides are named vibe 1–25. In varv A/kalata S and vibe 24 transcripts, two repeating mature domains are present. In acyclotides, either the conserved Asn/Asp or CTPP sequence is absent. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 1 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 1. Example structures and sequences from the three main cyclotide subfamilies. The structures are based on the PDB files for kalata B1 (1nb1), cycloviolacin O1 (1nbj) and Momordica cochinchinensis II (MCoTI-II) (1ib9). The unique cyclic cystine knot (CCK) topology of cyclotides arises when the ring formed by CysI-CysIV and CysII-CysV together with the backbone loops 1 and 4 are penetrated by the third disulfide between CysIII and CysVI. The cyclotide producing plant families are denoted by RRubiaceae VViolaceae, FFabaceae, SSolanaceae and CCucurbitaceae. The conserved Cys residues are highlighted in yellow and the cis-pro in loop 5 that defines the M¨obius subfamily is highlighted in blue. The conserved Asn/Asp residue at which cyclisation occurs is highlighted in red. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

Fig. 5 in Tropical vibes from Sri Lanka - cyclotides from Viola betonicifolia by transcriptome and mass spectrometry analysis

Fig. 5. Multiple sequence alignment of vibe AEPs and other functionally verified ligase- and protease-type AEPs identified in cyclic peptide producing plants. The AEP conserved catalytic triad residues Asn, Cys and His are highlighted in red. In the aligned AEPs, ligase activity determinant 1 (LAD1) containing gate keeper residue (highlighted in green/cyan, position orthologous to CYS247 in OaAEP1b (Harris et al., 2015) and ligase activity determinant 2 (LAD2) regions (highlighted in pink/blue) (Hemu et al., 2019), poly-proline region (Jackson et al., 2018) and marker of ligase activity region (MLA) (Jackson et al., 2018) are highlighted in boxes. VyPAL2 from V. yedoensis (Hemu et al., 2019), HeAEP3 from H. enneaspermus (Jackson et al., 2018), OaAEP1b from O. affinis (Harris et al., 2015) and butelase 1 from C. ternatea (Nguyen et al., 2014) are functionally verified ligases. MCoAEP2 has also shown efficient in vitro ligase activity, despite the presence of protease-type ligase activity determinant regions (Du et al., 2020). VyAEP1 from V. yedoensis and HaAEP1 from H. annus are protease-type AEPs with weaker ligase activity at high/neural pH (Haywood et al., 2018; Hemu et al., 2019). (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)

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Fig. 2 in Detection of candidate proteins in the indican biosynthetic pathway of Persicaria tinctoria (Polygonum tinctorium) using protein-protein interactions and transcriptome analyses

Fig. 2. Analysis of the protein–protein interaction using co-immunoprecipitation. Cytosolic (a) and microsomal fractions (b) were incubated with an anti-PtIGS antibody bound to the AminoLink Plus Coupling Resin. After elution with an acidic buffer, proteins were separated by SDS-PAGE using a 12.5% acrylamide gel for (a) and 10% for (b). After the samples corresponding to (a) 0.205 and (b) 0.057 g wet weight leaves were analyzed, total proteins were visualized with silver staining. As the control, PtIGS in the samples corresponding to 0.041 and 0.057 g wet weight leaves was also detected with western blotting using the anti-PtIGS antibody. C1–C6 and M1–M10 show the regions that were cut from gels and subjected to MS/MS analysis. The symbols "+" and "-" represent the use of AminoLink Plus Coupling Resins bound with anti-PtIGS antibody and without antibody, respectively.

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Fig. 1 in Detection of candidate proteins in the indican biosynthetic pathway of Persicaria tinctoria (Polygonum tinctorium) using protein-protein interactions and transcriptome analyses

Fig. 1. Chemical crosslinking assay in vitro and in vivo. Cytosolic (a) and microsomal (b) fractions and the protoplasts (c) were treated with chemical crosslinkers (BS3 and DSS, respectively). Treated samples were then subjected to SDS-PAGE using a 10% acrylamide gel for (a) and (b) and 7.5% for (c). Proteins that reacted against the anti-PtIGS antibody were detected by western blotting. "I" indicates PtIGS monomer. "II" denotes molecules larger than the monomer.