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Fig. 1 in Flavonoid biosynthesis in Dianthus caryophyllus L. is early regulated during interaction with Fusarium oxysporum f. sp. dianthi

Fig. 1. Three-phase workflow performed in this study. Each colored segment comprises the general steps (in boxes) adopted in each study phase. hpi = hours postinoculation. TPC = Total phenolic content. TFC = Total flavonoid content.

Fig. 4 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 4. The biochemical pathway to schizokinen. The established route to rhizobactin 1021 in Sinorhizobium meliloti (Lynch et al., 2001) includes schizokinen as its immediate precursor. (The enzyme responsible for the biosynthesis of rhizobactin 1021 from schizokinen is currently unknown). Nomenclature is from www.bren da-enzymes.org. The genes rhbA and rhbB (Lynch et al., 2001), correspond to the enzymes diaminobutanoate-2-oxo-glutarate transaminase (RhbA, EC 2.6.1.76) and diaminobutanoate decarboxylase (RhbB, EC 4.1.1.86). The enzymes RhbD (an acetylase), RhbE (which catalyses the oxidation of a single amino group of 1,3-diaminopropane), RhbC and RhbF (which catalyse condensation reactions) are unclassified. Redrawn from Lynch et al. (2001). The molecule in square brackets* represents 2,4-diaminobutanoate (2,4-diaminobutanoic acid) after rotation of the amino and carboxylate functions about carbon-2 to allow visual alignment of the amino groups in 1,3-diaminopropane and subsequent derivatives.

Fig. 8 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 8. The localisation of the enzymes diaminobutanoate-2-oxo-glutarate transaminase, the downstream decarboxylase, and ectoine synthase within siderophore clusters and incomplete ectoine clusters. The top three clusters correspond to NIS clusters and the bottom cluster corresponds to an incomplete ectoine cluster. The organisation of NIS clusters follows the same pattern: diaminobutanoate-2-oxo-glutarate transaminase (EC 2.6.1.76), followed by diaminobutanoate decarboxylase (EC 4.1.1.86) and IucA/IucC (EC 6.3.2.38, EC 6.3.2.39) family siderophore biosynthesis protein. Arrows point to the orientation of transcription. AntiSMASH was used to identify and annotate specialised metabolite clusters containing both 2,4-DAB transaminase and decarboxylase or 2,4-DAB transaminase and ectoine synthase (EC 4.2.1.108).

Fig. 3 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 3. The synthesis of 1,3-diaminopropane from 2,4-DAB. Established route to 1,3-diaminopropane. The nomenclature is from www.brenda-enzymes.org; the Enzyme Commission numbers are as follows: (1) diaminobutanoate-2-oxo-glutarate transaminase: EC 2.6.1.76; (2) diaminobutanoate decarboxylase: EC 4.1.1.86.

Fig. 2. The aspartate 4 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 2. The aspartate 4-phosphate pathway. Established routes to 2,4-diaminobutanoate (2,4-diaminobutanoic acid) and derivatives. The nomenclature is from www.brenda-enzymes.org; the Enzyme Commission numbers are as follows: (1) aspartate transaminase: EC 2.6.1.1; (2) aspartate kinase: EC 2.7.2.4; (3) aspartate-semialdehyde dehydrogenase: EC 1.2.1.11; (4) diaminobutanoate- 2-oxo-glutarate transaminase: EC 2.6.1.76; (5) diaminobutanoate acetyltransferase: EC 2.3.1.178; (6) ectoine synthase: EC 4.2.1.108; and (7) ectoine hydroxylase: EC 1.14.11.55. Multiple-step pathways are indicated by *.

Fig. 1 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 1. Structure of 2,4-diaminobutanoic acid in the ionised form (2,4- diaminobutanoate). This form is present at physiological pH values. The carboxyl group is then completely ionised and positive charge is shared between the two amino groups.

Fig. 6 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 6. The pathway to 2,4-DAB derived from S-adenosylmethionine (SAM). The formation of 2,4-diaminobutanoate (2,4-diaminobutanoic acid) from S-adenosylmethionine (SAM) and isoxazolin-5-one in Lathyrus sylvestris (Callebaut and Lambein, 1977; Ikegami and Murakoshi, 1994). ACI: 2-(3-amino-3-carboxypropyl)-isoxazolin-5-one (Kuo et al., 1982). The enzymes catalysing the two reactions are unclassified.

Fig. 7 in Genomic insights into the biosynthesis and physiology of the cyanobacterial neurotoxin 2,4-diaminobutanoic acid (2,4-DAB)

Fig. 7. Species phylogeny showing the cross-species distribution of specialised metabolite clusters containing a gene coding for diaminobutanoate-2-oxoglutarate transaminase (EC 2.6.1.76). The enzymes encoded by each species are indicated by coloured circles, next to the species name. For enzymes' accession numbers, see Supplementary Tables S12-S17. See Supplementary Fig. S2 for bootstrap support of each branch.

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Fig. 5 in Protochlorophylls in Cucurbitaceae - Distribution, biosynthesis and phylogeny

Fig. 5. Composition of protochlorophylls in primary leaves of 11-day-old etiolated Cucurbita pepo 'Miranda' and C. maxima 'Bambino' seedlings during illumination. In the case of ALA-treated plants, the 11-day-old seedlings were incubated for additional 3 days in 10 mM ALA solution in the dark before illumination. The data are means ± SE, n = 3–4. The pigments were extracted and analyzed using HPLC as described in the Experimental section.

Fig. 9 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 9. Evolutionary relationships of susL, rolD homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 4.915 shown. The analysis involved 37 nucleotide sequences. There were a total of 137 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 5 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 5. Evolutionary relationships of cus homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 2.438 is shown. The analysis involved 41 nucleotide sequences. There were a total of 354 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 2 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 2. Evolutionary relationships of ags(*) and chs(**) homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 1.404 is shown. The analysis involved 12 nucleotide sequences. There were a total of 647 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 4 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 4. Evolutionary relationships of mas2′ homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 3.135 is shown. The analysis involved 24 nucleotide sequences. There were a total of 874 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 8 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 8. Evolutionary relationships of vis and ocs homologs in Agrobacterium and plants. The vis and ocs genes are indicated with * and ** respectively. Genes marked in bold code for well-characterized enzymes, the underlined gene is marked as ocs based on its high sequence similarity to other ocs genes. The optimal tree with the sum of branch length = 2.875 is shown. The analysis involved 21 nucleotide sequences. There were a total of 1056 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 7 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 7. Evolutionary relationships of nos homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 2.895 is shown. The analysis involved 11 nucleotide sequences. There were a total of 708 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 6 in Opine biosynthesis in naturally transgenic plants: Genes and products

Fig. 6. Evolutionary relationships of mis homologs in Agrobacterium and plants. The optimal tree with the sum of branch length = 1.968 is shown. The analysis involved 33 nucleotide sequences. There were a total of 660 positions in the final dataset. Further details as in the legend to Fig. 1.

Fig. 4 in Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm

Fig. 4. The relative transcript levels of RlMTPSLs determined by qRT-PCR. The transcript levels of four RlMTPSL genes were calculated relative to the expression of the β-actin gene. Error bars represent the SD of at least three independent experiments.

Fig. 1 in Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm

Fig. 1. Chemical profiling of R. lindenbergiana. 5, striatene; 6, pentalenene; 8, α-funebrene; 9, β-elemene; 10, petasitene; 11, α-cedrene; 12, isobazzanene; 13, (E)-α-bergamotene; 14, epi-β-santalene; 15, (E)-β-farnesene; 17, β-santalene; 18, β-acoradiene; 19, 4,5-di-epi-aristolochene; 20, ar-curcumene; 21, unidentified sesquiterpene; 22, eremophilene; 23, α-selinene; 24, (E,E)-α-farnesene and β-curcumene; 25, (Z)-β-bisabolene; All listed compounds are tentatively identified using mass spec libraries. All numbered compounds that are not listed represent unidentified sesquiterpenes.

Fig. 5 in Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm

Fig. 5. Phylogenetic tree of MTPSLs from Radula lindenbergiana, Anthoceros, Selaginella moellendorffii, and Marchantia polymorpha. Species: Radula lindenbergiana (Rl), Anthoceros agrestis (Aa), Anthoceros punctatus (Ap), Selaginella moellendorffii (Sm), and Marchantia polymorpha (Mp). The analysis included 5 MTPSLs from R. lindenbergiana, 7 MTPSLs from A. punctatus, 6 MTPSLs from A. agrestis, 9 MTPSLs from M. polymorpha, and 48 MTPSLs from S. moellendorffii.

Fig. 2 in Sesquiterpene biosynthesis in a leafy liverwort Radula lindenbergiana Gottsche ex C. Hartm

Fig. 2. GC-MS analysis of sesquiterpenes produced by recombinant RlMTPSL1, RlMTPSL2, RlMTPSL3, and RlMTPSL4, respectively. (A) The enzymes were expressed in E. coli, extracted, and incubated with the substrate (E,E)-farnesyl diphosphate (FPP). Peak numbers are used as listed in Fig. 1. 5, striatene; 6, pentalenene; 8, α-funebrene; 9, β-elemene; 10, petasitene; 11, α-cedrene; 12, isobazzanene; 13, (E)- α-bergamotene; 14, epi-β-santalene; 15, (E)-β-farnesene; 17, β-santalene; 18, β-acoradiene; 19, 4,5-di-epi- aristolochene; 20, ar-curcumene; 21, unidentified sesquiterpene; 22, eremophilene; 23, α-selinene; 24, (E,E)-α-farnesene and β-curcumene; 25, (Z)-β-bisabolene; 29, indole (contamination from E. coli). All numbered compounds that are not listed represent unidentified sesquiterpenes. (B) Structures of representative RIMTPSL enzyme products.