baccatin iii (MedChemExpress)

MedChemExpress baccatin iii

( a ) Heat map showing the ranks of new T9α H and T1βHs and other Taxol biosynthetic genes in the <t>three</t> modules. T9αH-725A is the T9αH independently reported by other groups.8–10 ( b ) Proposed biosynthetic pathway from 4 , the latest intermediate we reported recently,13 to taxusin ( 6 ) and the corresponding extracted ion chromatograms (EICs) of products 4-6 when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol, which only involves 4 and 5 . ( c ) Proposed biosynthetic pathway from 5 to <t>baccatin</t> VI ( 11-Bz ) and the corresponding EICs of intermediates when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol. Structures of 5 , 7-Ac , 7-Bz , 8-Ac , 8-Bz , 9-Ac , 9-Bz , 10-Ac , 10-Bz , 11-Ac are proposed based on functions of enzymes previously characterized (TAT, TAX19, T2αH, TBT, T7βH, and TOT) and described in this study (Τ9αH-750C, T7AT, and T1βH). TAX19 are used to generate known 13-O-acetylated products, including taxusin ( 6 ) and baccatin VI ( 11-Bz ), for structural analysis. ( d ) EICs of expected products when the pathway to 6O4A is expressed with TOT, T7AT, or both in N. benthamiana . In the absence of T7AT, no significant 6O4A depletion or product formation by TOT is observed. ( e ) MSMS fragmentation patterns of heterologously produced baccatin VI ( 11-Bz ) in N. benthamiana compared to that of 11-Bz standard. MSMS fragmentations were generated using [M+Na]+ (m/z = 737.2788) as the precursor ion and fragmented with a collision energy of 30 eV.

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( a ) Heat map showing the ranks of new T9α H and T1βHs and other Taxol biosynthetic genes in the three modules. T9αH-725A is the T9αH independently reported by other groups.8–10 ( b ) Proposed biosynthetic pathway from 4 , the latest intermediate we reported recently,13 to taxusin ( 6 ) and the corresponding extracted ion chromatograms (EICs) of products 4-6 when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol, which only involves 4 and 5 . ( c ) Proposed biosynthetic pathway from 5 to baccatin VI ( 11-Bz ) and the corresponding EICs of intermediates when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol. Structures of 5 , 7-Ac , 7-Bz , 8-Ac , 8-Bz , 9-Ac , 9-Bz , 10-Ac , 10-Bz , 11-Ac are proposed based on functions of enzymes previously characterized (TAT, TAX19, T2αH, TBT, T7βH, and TOT) and described in this study (Τ9αH-750C, T7AT, and T1βH). TAX19 are used to generate known 13-O-acetylated products, including taxusin ( 6 ) and baccatin VI ( 11-Bz ), for structural analysis. ( d ) EICs of expected products when the pathway to 6O4A is expressed with TOT, T7AT, or both in N. benthamiana . In the absence of T7AT, no significant 6O4A depletion or product formation by TOT is observed. ( e ) MSMS fragmentation patterns of heterologously produced baccatin VI ( 11-Bz ) in N. benthamiana compared to that of 11-Bz standard. MSMS fragmentations were generated using [M+Na]+ (m/z = 737.2788) as the precursor ion and fragmented with a collision energy of 30 eV.

Journal: bioRxiv

Article Title: Multiplexed perturbation of yew reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors

doi: 10.1101/2024.11.06.622305

Figure Lengend Snippet: ( a ) Heat map showing the ranks of new T9α H and T1βHs and other Taxol biosynthetic genes in the three modules. T9αH-725A is the T9αH independently reported by other groups.8–10 ( b ) Proposed biosynthetic pathway from 4 , the latest intermediate we reported recently,13 to taxusin ( 6 ) and the corresponding extracted ion chromatograms (EICs) of products 4-6 when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol, which only involves 4 and 5 . ( c ) Proposed biosynthetic pathway from 5 to baccatin VI ( 11-Bz ) and the corresponding EICs of intermediates when the indicated sets of genes were expressed in N. benthamiana leaves. Blue shade highlights the biosynthetic pathway toward Taxol. Structures of 5 , 7-Ac , 7-Bz , 8-Ac , 8-Bz , 9-Ac , 9-Bz , 10-Ac , 10-Bz , 11-Ac are proposed based on functions of enzymes previously characterized (TAT, TAX19, T2αH, TBT, T7βH, and TOT) and described in this study (Τ9αH-750C, T7AT, and T1βH). TAX19 are used to generate known 13-O-acetylated products, including taxusin ( 6 ) and baccatin VI ( 11-Bz ), for structural analysis. ( d ) EICs of expected products when the pathway to 6O4A is expressed with TOT, T7AT, or both in N. benthamiana . In the absence of T7AT, no significant 6O4A depletion or product formation by TOT is observed. ( e ) MSMS fragmentation patterns of heterologously produced baccatin VI ( 11-Bz ) in N. benthamiana compared to that of 11-Bz standard. MSMS fragmentations were generated using [M+Na]+ (m/z = 737.2788) as the precursor ion and fragmented with a collision energy of 30 eV.

Article Snippet: Chemical standards are purchased from the following vendors (with catalog number listed): taxusin (TargetMol; TN6763), 1-hydroxybaccatin I (LKT Labs; T0092), baccatin VI (Santa Cruz Biotechnology; sc-503244), 10-deacetylbaccatin III (Sigma-Aldrich; D3676), baccatin III (MedChemExpress; HY-N6985), 9-dihydro-13-acetylbaccatin III (TargetMol; T5132).

Techniques: Produced, Generated

( a ) Simplified representation of biosynthetic transformations from taxadiene ( 1 ) to baccatin III ( 16 ) with coordinates showing the decoration state (i.e. acylation and oxidation) on the taxadiene ( 1 ) scaffold. Importantly, two deacetylations and one oxidation are required to go from intermediate 10-Bz to baccatin III (16). Taxanes with C-13 acetoxy, including taxusin ( 6 ) and baccatin VI ( 11-Bz ), are not biosynthetic intermediates to baccatin III ( 16 ). ( b ) Characterization of the two deacetylases, DeAc 898 and 1023, by feeding baccatin VI ( 11-Bz ) to N. benthamiana leaves expressing GFP, DeAc 898 and DeAc 1023. EICs of 11-Bz, the corresponding mono-deacetylated product 12 and di-deacetylated product 9-dihydro-13-acetyl-baccatin III (9DHAB, 13 ) are shown. ( c ) Proposed biosynthetic pathway from 10-Bz to baccatin III ( 16 ) via taxane 9α-O-deacetylase (T9dA; DeAc 898), T9ox, and taxane 7β-O-deacetylase (T7dA; DeAc 1023) and the EICs of intermediates when the indicated sets of genes were expressed in N. benthamiana leaves. ( d ) MSMS fragmentation patterns of heterologously produced baccatin III (16) in N. benthamiana compared to that of 16 standard. MSMS fragmentations were generated using [M+Na]+ (m/z = 609.2313) as the precursor ion and fragmented with a collision energy of 30 eV. ( e ) Proposed side-chain formation and biosynthetic pathway from baccatin III ( 16 ) to Taxol. Phenylalanine aminomutase (PAM) ‘and PCL convert phenylalanine (Phe) to β-Phe-CoA, which is installed onto baccatin III by baccatin III:3-amino-3-phenylpropanoyl transferase (BAPT) to yield 3’-N-debenzoyl-2’-deoxypaclitaxel ( 17 ). While taxane 2’α-hydroxylase (T2’αΗ) and 3′-N-debenzoyl-2′-deoxypaclitaxel-N-benzoyl transferase (DBTNBT) have been previously reported, we were not able to recapitulate their enzymatic activities to complete biosynthetic pathway to Taxol. Only DBTNBT showed activity, and low efficiency suggests that the 2’α-hydroxylation may need to occur first. ( f ) Heatmap showing the ranks of T9ox, side-chain enzymes and PCL candidates in gene modules. The active PCL (867.5) is indicated in magenta. ( g ) 3’-N-debenzoyl-2’-deoxypaclitaxel ( 17 ) can be produced either by feeding baccatin III ( 16 ) to N. benthamiana leaves expressing the three side-chain biosynthetic genes (PAM, PCL, and BAPT) or by heterologously expressing the complete biosynthetic gene set to baccatin III (16) plus the three side-chain biosynthetic genes. EICs of 16 and 17 are shown.

Journal: bioRxiv

Article Title: Multiplexed perturbation of yew reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors

doi: 10.1101/2024.11.06.622305

Figure Lengend Snippet: ( a ) Simplified representation of biosynthetic transformations from taxadiene ( 1 ) to baccatin III ( 16 ) with coordinates showing the decoration state (i.e. acylation and oxidation) on the taxadiene ( 1 ) scaffold. Importantly, two deacetylations and one oxidation are required to go from intermediate 10-Bz to baccatin III (16). Taxanes with C-13 acetoxy, including taxusin ( 6 ) and baccatin VI ( 11-Bz ), are not biosynthetic intermediates to baccatin III ( 16 ). ( b ) Characterization of the two deacetylases, DeAc 898 and 1023, by feeding baccatin VI ( 11-Bz ) to N. benthamiana leaves expressing GFP, DeAc 898 and DeAc 1023. EICs of 11-Bz, the corresponding mono-deacetylated product 12 and di-deacetylated product 9-dihydro-13-acetyl-baccatin III (9DHAB, 13 ) are shown. ( c ) Proposed biosynthetic pathway from 10-Bz to baccatin III ( 16 ) via taxane 9α-O-deacetylase (T9dA; DeAc 898), T9ox, and taxane 7β-O-deacetylase (T7dA; DeAc 1023) and the EICs of intermediates when the indicated sets of genes were expressed in N. benthamiana leaves. ( d ) MSMS fragmentation patterns of heterologously produced baccatin III (16) in N. benthamiana compared to that of 16 standard. MSMS fragmentations were generated using [M+Na]+ (m/z = 609.2313) as the precursor ion and fragmented with a collision energy of 30 eV. ( e ) Proposed side-chain formation and biosynthetic pathway from baccatin III ( 16 ) to Taxol. Phenylalanine aminomutase (PAM) ‘and PCL convert phenylalanine (Phe) to β-Phe-CoA, which is installed onto baccatin III by baccatin III:3-amino-3-phenylpropanoyl transferase (BAPT) to yield 3’-N-debenzoyl-2’-deoxypaclitaxel ( 17 ). While taxane 2’α-hydroxylase (T2’αΗ) and 3′-N-debenzoyl-2′-deoxypaclitaxel-N-benzoyl transferase (DBTNBT) have been previously reported, we were not able to recapitulate their enzymatic activities to complete biosynthetic pathway to Taxol. Only DBTNBT showed activity, and low efficiency suggests that the 2’α-hydroxylation may need to occur first. ( f ) Heatmap showing the ranks of T9ox, side-chain enzymes and PCL candidates in gene modules. The active PCL (867.5) is indicated in magenta. ( g ) 3’-N-debenzoyl-2’-deoxypaclitaxel ( 17 ) can be produced either by feeding baccatin III ( 16 ) to N. benthamiana leaves expressing the three side-chain biosynthetic genes (PAM, PCL, and BAPT) or by heterologously expressing the complete biosynthetic gene set to baccatin III (16) plus the three side-chain biosynthetic genes. EICs of 16 and 17 are shown.

Techniques: Expressing, Histone Deacetylase Assay, Produced, Generated, Activity Assay

( a ) Ranks of new Taxol biosynthetic gene discovered in this paper by Pearson correlation coefficient (PCC) to TDS using either bulk or mpXsn data. New data from mpXsn was crucial for prioritizing all new Taxol genes except T9dA. Newly discovered genes are indicated in orange (anticipated discovery) and pink (unexpected discovery). ( b ) Heatmap showing the ranks of updated Taxol biosynthetic pathway in the models. ( c ) Baccatin III ( 16 ) yields in μg/g dried weight (DW), quantified with standards on a triple quadrupole mass spectrometer ( Methods ), of our 17-gene baccatin III pathway with each single-gene dropout tested in N. benthamiana . All genes are crucial for significant baccatin III ( 16 ) yield except T5αH. Baccatin III ( 16 ) yields from replicating published gene sets , as well as from T. media needle are shown for comparison. Data are shown as the mean ± standard deviation, n = 3 biological replicates. ( d ) EIC showing the di-oxidized taxadiene product when T13αΗ is expressed with TDS, and its production is boosted by FoTO1 ( Fig. S26 ). Adding TAX19, acyltransferase previously characterized to be specific for taxane C-5α- and C-13α-O-acetylation, results in the production of a diacetoxytaxadiene ( Fig. S27 ). This leads us to propose that T13αH is able to produce taxadien-5α,13α-diol, thus complementing T5αH. ( e ) Five pairs of functional redundant enzymes in the Taxol biosynthetic pathway with their single-cell expression patterns, percentage identity (% ID) in protein sequence, and protein structures or phylogenetic trees shown. Crystal structure of TDS1 (PDB 3P5P) and the AlphaFold3 predicted structure of TDS2 are shown. Phylogenetic trees of the three main tailoring enzyme families involved in Taxol biosynthesis — P450s, 2-ODDs, and acyltransferases. Protein sequences from each family were aligned using Clustal Omega, and the phylogenetic trees were constructed using the neighbor-joining method in Geneious Prime with 1,000 bootstrap replicates. AtC4H, AtGA20ox1, and HvACT were selected as outgroups for each family. ( f ) Summary of the Taxol biosynthesis and the reconstituted C-13α-acetoxy taxane biosynthesis in this study. Blue shade indicates our reconstituted pathway to baccatin III ( 16 ) and the proposed transformations to Taxol. Co-expression of TAX19 with partial pathways leads to C-13α-acetoxy taxanes including taxusin ( 6 ), baccatin VI ( 11-Bz ), and 9DHAB ( 13 ) that can be confirmed with chemical standards ( , S9, S19). Structures are proposed based on high resolution MS (HRMS), confirmed by NMR, and/or confirmed by HRMS/MS comparison to standards. Dotted arrow indicated previously reported biosynthetic transformations that we failed to reproduce.

Journal: bioRxiv

Article Title: Multiplexed perturbation of yew reveals cryptic proteins that enable a total biosynthesis of baccatin III and Taxol precursors

doi: 10.1101/2024.11.06.622305

Figure Lengend Snippet: ( a ) Ranks of new Taxol biosynthetic gene discovered in this paper by Pearson correlation coefficient (PCC) to TDS using either bulk or mpXsn data. New data from mpXsn was crucial for prioritizing all new Taxol genes except T9dA. Newly discovered genes are indicated in orange (anticipated discovery) and pink (unexpected discovery). ( b ) Heatmap showing the ranks of updated Taxol biosynthetic pathway in the models. ( c ) Baccatin III ( 16 ) yields in μg/g dried weight (DW), quantified with standards on a triple quadrupole mass spectrometer ( Methods ), of our 17-gene baccatin III pathway with each single-gene dropout tested in N. benthamiana . All genes are crucial for significant baccatin III ( 16 ) yield except T5αH. Baccatin III ( 16 ) yields from replicating published gene sets , as well as from T. media needle are shown for comparison. Data are shown as the mean ± standard deviation, n = 3 biological replicates. ( d ) EIC showing the di-oxidized taxadiene product when T13αΗ is expressed with TDS, and its production is boosted by FoTO1 ( Fig. S26 ). Adding TAX19, acyltransferase previously characterized to be specific for taxane C-5α- and C-13α-O-acetylation, results in the production of a diacetoxytaxadiene ( Fig. S27 ). This leads us to propose that T13αH is able to produce taxadien-5α,13α-diol, thus complementing T5αH. ( e ) Five pairs of functional redundant enzymes in the Taxol biosynthetic pathway with their single-cell expression patterns, percentage identity (% ID) in protein sequence, and protein structures or phylogenetic trees shown. Crystal structure of TDS1 (PDB 3P5P) and the AlphaFold3 predicted structure of TDS2 are shown. Phylogenetic trees of the three main tailoring enzyme families involved in Taxol biosynthesis — P450s, 2-ODDs, and acyltransferases. Protein sequences from each family were aligned using Clustal Omega, and the phylogenetic trees were constructed using the neighbor-joining method in Geneious Prime with 1,000 bootstrap replicates. AtC4H, AtGA20ox1, and HvACT were selected as outgroups for each family. ( f ) Summary of the Taxol biosynthesis and the reconstituted C-13α-acetoxy taxane biosynthesis in this study. Blue shade indicates our reconstituted pathway to baccatin III ( 16 ) and the proposed transformations to Taxol. Co-expression of TAX19 with partial pathways leads to C-13α-acetoxy taxanes including taxusin ( 6 ), baccatin VI ( 11-Bz ), and 9DHAB ( 13 ) that can be confirmed with chemical standards ( , S9, S19). Structures are proposed based on high resolution MS (HRMS), confirmed by NMR, and/or confirmed by HRMS/MS comparison to standards. Dotted arrow indicated previously reported biosynthetic transformations that we failed to reproduce.

Techniques: Targeted Proteomics, Mass Spectrometry, Comparison, Standard Deviation, Functional Assay, Single Cell, Expressing, Sequencing, Construct

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