Harnessing photoenzymatic reactions for unnatural biosynthesis in microorganisms
Data files
Dec 10, 2025 version files 77 MB
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pACYC_receiver.dna
129.03 KB
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pET-30a(_)_-_OYE1.dna
797.70 KB
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pML13_(pET30a(_)-T7-OYE3_N194Y-T7-PntAB).dna
936.20 KB
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pML14_(pET30a(_)-T7-OYE3_N194Y-T7-UdhA).dna
914.15 KB
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pML15_(pET30a(_)-T7-OYE3_N194Y-T7-Icd).dna
921.98 KB
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pML16_(pET30a(_)-T7-OYE3_N194Y-T7-GapC).dna
929.66 KB
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pML17_(pET30a(_)-T7-OYE3_N194Y-T7-PTDH_mutant).dna
939.11 KB
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pML18_(pET30a(_)-T7-OYE3_N194Y-T7-BstFDH_mutant).dna
947.72 KB
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pML19_(pET30a(_)-T7-OYE3_N194Y-Trc-GDH).dna
928.22 KB
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pML22_(pET30a(_)-T7-OYE3_N194Y-Trc-Icd).dna
932.69 KB
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pML23_(pET30a(_)-T7-OYE3_N194Y-lac-GDH).dna
941.94 KB
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pML26_(pET30a(_)-T7-OYE3_N194Y-lac-Icd).dna
941.88 KB
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pML35_(pET30a(_)-TRC-OYE3_N194Y-T7-GDH).dna
925.92 KB
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pML38_(pET30a(_)-TRC-OYE3_N194Y-T7-Icd).dna
932.09 KB
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pML39_(pET30a(_)-TRC-OYE3_N194Y-lac-GDH).dna
958.28 KB
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pML42_(pET30a(_)-TRC-OYE3_N194Y-lac-Icd).dna
953.48 KB
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pML43_(pET30a(_)-vector).dna
902.77 KB
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pML7_(pET30a(_)-T7-OYE3_N194Y-T7-GDH).dna
911.71 KB
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pML70_(pET30a(_)-TRC-OYE3_N194Y-lac-GDH-no_tag).dna
1.07 MB
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pML71_(pET30a(_)-TRC-OYE3_N194Y-lac-Icd-no_tag).dna
1 MB
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pML8_(pET30a(_)-T7-OYE3_N194Y-T7-zwf).dna
919 KB
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pML81_(pET30a(_)-TRC-OYE1-lac-GDH).dna
1.14 MB
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pML82_(pET30a(_)-TRC-OYE1-lac-Icd).dna
1.05 MB
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pML83_(pET30a(_)-TRC-OYE1_H191A-lac-GDH).dna
1.12 MB
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pML84_(pET30a(_)-TRC-OYE1_H191A-lac-Icd).dna
1.02 MB
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pML85_(pET30a(_)-TRC-OYE1_Y82F-lac-GDH).dna
1.14 MB
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pML86_(pET30a(_)-TRC-OYE1_Y82F-lac-Icd).dna
1.06 MB
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pML89_(pET30a(_)-TRC-GluER_T36E_W66F_F68Y_P263L_F269Y_Q293T-lac-GDH).dna
1.25 MB
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pML9_(pET30a(_)-T7-OYE3_N194Y-T7-pos5).dna
928.41 KB
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pML90_(pET30a(_)-TRC-GluER_T36E_W66F_F68Y_P263L_F269Y_Q293T-lac-Icd).dna
1.11 MB
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pYJ700_(pET30a(_)-OYE1-GDH).dna
844.69 KB
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pYJ702_(pET30a(_)-OYE1-Pos5).dna
856.82 KB
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pYJ727_(pET30a-Ptrc-PALY_RHOTO-PadA_LACPL-ppsA-tktA).dna
871.27 KB
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pYJ728_(pACYC_aroF-tyrA).dna
791.34 KB
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pYJ729_(pRSFDuet_Amp__Plac-tnaA).dna
1.54 MB
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pYJ749_(4-vinylphenol_biosynthetic_genes_(pACYC-aroF-tyrA__Plac__T7p__PALY_RHOTO__PadA_LACPL__ppsA__tktA)).dna
1.07 MB
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pYJ750_(styrene_biosynthetic_genes_(pACYC-aroF-pheA__T7p__Ptrc__PAL2__FDC1__ppsA__tktA)).dna
983.35 KB
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pYJ751_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori).dna
1.08 MB
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pYJ753_(pET30a-aroF-pheA__T7p__Ptrc__PAL2__FDC1__ppsA__tktA__pBR322_ori).dna
1.11 MB
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pYJ755_(pACYC_vector__Chl__Plac-tnaA).dna
267.80 KB
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pYJ761_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori__Trc-OYE3_N194Y__Lac-GDH).dna
1.23 MB
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pYJ762_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori__Trc-OYE3_N194Y__Lac-Icd).dna
1.13 MB
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pYJ763_(pRSF_ori__Trc-OYE3_N194Y__Lac-GDH).dna
1.68 MB
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pYJ764_(pRSF_ori__Trc-OYE3_N194Y__Lac-Icd).dna
1.80 MB
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pYJ767_(pRSF_ori__Trc-OYE1__Lac-GDH).dna
1.80 MB
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pYJ768_(pRSF_ori__Trc-OYE1_H191A__Lac-GDH).dna
1.92 MB
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pYJ769_(pRSF_ori__Trc-OYE1_Y82F__Lac-GDH).dna
2.04 MB
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pYJ770_(pRSF_ori__Trc-GluER_M6__Lac-GDH).dna
2.17 MB
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pYJ771_(pRSF_ori__Trc-OYE1__Lac-Icd).dna
2.04 MB
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pYJ772_(pRSF_ori__Trc-OYE1_H191A__Lac-Icd).dna
2.15 MB
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pYJ773_(pRSF_ori__Trc-OYE1_Y82F__Lac-Icd).dna
2.27 MB
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pYJ774_(pRSF_ori__Trc-GluER_M6__Lac-Icd).dna
2.40 MB
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pYJ775_(pRSF_ori__T7-OYE1-Y82G_T37Q).dna
1.90 MB
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pYJ776_(pRSF_ori__T7-OYE1-WT).dna
2.01 MB
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pYJ777_(pRSF_ori__T7-OYE1-Y82G).dna
2.13 MB
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pYJ779_(pRSF_ori__T7-OYE1-Y82G_T37Q_W116A_H191S).dna
2.48 MB
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pYJ783_(p15A_CmR-araBAD-TnaA).dna
2.20 MB
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pYJ784_(pET30a(_)-T7-OYE3_N194Y-T7-GDH-ICD).dna
948.12 KB
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pYJ785_(pET30a(_)-T7-OYE3_N194Y-T7-Icd-GDH).dna
937.73 KB
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pYJ786_(pRSF_ori__Lac-GDH).dna
1.78 MB
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pYJ787_(pRSF_ori__Lac-Icd).dna
1.90 MB
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README.md
8.10 KB
Abstract
Photoenzymatic catalysis enables new-to-nature transformations, but its scalability is limited by high enzyme loading, costly cofactors, and radical-induced instability. Here we report the integration of light-driven photoenzymatic reactions into the cellular metabolism of Escherichia coli, bridging flavin-based photobiocatalysis with biosynthesis. Using synthetic biology strategies, we engineered microbial cells to continuously produce olefin substrates and ene-reductase photoenzyme while regenerating cofactors directly from glucose. By externally supplying radical precursors or by introducing synthetic pathways for their in situ production, we enabled fermentation-based microbial photobiosynthesis, achieving high titers and demonstrating its feasibility for scale-up in bioreactor. This approach extends photobiocatalysis from in vitro applications to in vivo semi-biosynthesis and complete biosynthesis, revealing its full potential for integrating light-driven reactions into cellular metabolism.
Dataset DOI: 10.5061/dryad.ns1rn8q54
Description of the data and file structure
This dataset supports the research published in “Harnessing Photoenzymatic Reactions for Unnatural Biosynthesis in Microorganisms”. It includes all the necessary SnapGene files for the plasmids described in the article and the Supplementary Information. All files are provided in SnapGene (.dna) format and can be opened and edited using SnapGene or SnapGene Viewer.
OYE family enzymes (Old Yellow Enzymes / ene-reductases)
Auxiliary NADPH-regeneration systems
Promoter comparisons (T7, Trc, lac)
4-vinylphenol and styrene biosynthetic pathway construction
Photobiocatalysis pathways (using photoenzymes + NADPH regeneration)
Whole-cell screening of OYE mutants
pACYC_receiver.dna
- A p15A-origin backbone is used as a general template for constructing new plasmids.
pML43_(pET30a(_)-vector).dna
- Empty pET-30a vector; used as a negative control.
pET-30a()-_OYE1.dna
Expresses OYE1.
Mutant or promoter-varied OYE plasmids (examples):
pML19, pML22, pML23, pML26 → OYE3_N194Y under T7 or Trc or lac promoters
pML35, pML38, pML39, pML42 → same as above but different promoter arrangement
pML81–pML86 → OYE1 variants (WT, H191A, Y82F) for substrate scope
pML89, pML90 → GluER_M6 variants for substrate scope
- pACYC_receiver.dna: p15A template
- pET-30a()-_OYE1.dna: OYE1 expression plasmid
- pML13_(pET30a(_)-T7-OYE3_N194Y-T7-PntAB).dna: Contains the PntAB gene, for NADPH regeneration
- pML14_(pET30a(_)-T7-OYE3_N194Y-T7-UdhA).dna: Contains the UdhA gene, for NADPH regeneration
- pML15_(pET30a(_)-T7-OYE3_N194Y-T7-Icd).dna: Contains the Icd gene, for NADPH regeneration
- pML16_(pET30a(_)-T7-OYE3_N194Y-T7-GapC).dna: Contains GapC gene, for NADPH regeneration
- pML17_(pET30a(_)-T7-OYE3_N194Y-T7-PTDH_mutant).dna: Contains the PTDH gene, for NADPH regeneration
- pML18_(pET30a(_)-T7-OYE3_N194Y-T7-BstFDH_mutant).dna: Contains the BstFDH gene, for NADPH regeneration
- pML19_(pET30a(_)-T7-OYE3_N194Y-Trc-GDH).dna: Contain T7-OYE3_N194Y and Trc-GDH, for promoters evaluation
- pML22_(pET30a(_)-T7-OYE3_N194Y-Trc-Icd).dna: Contain T7-OYE3_N194Y and Trc-Icd, for promoters evaluation
- pML23_(pET30a(_)-T7-OYE3_N194Y-lac-GDH).dna: Contain T7-OYE3_N194Y and lac-GDH, for promoters evaluation
- pML26_(pET30a(_)-T7-OYE3_N194Y-lac-Icd).dna: Contain T7-OYE3_N194Y and lac-Icd, for promoters evaluation
- pML35_(pET30a(_)-TRC-OYE3_N194Y-T7-GDH).dna: Contain TRC-OYE3_N194Y and T7-GDH, for promoters evaluation
- pML38_(pET30a(_)-TRC-OYE3_N194Y-T7-Icd).dna: Contain TRC-OYE3_N194Y and T7-Icd, for promoters evaluation
- pML39_(pET30a(_)-TRC-OYE3_N194Y-lac-GDH).dna: Contain TRC-OYE3_N194Y and lac-GDH, for promoters evaluation
- pML42_(pET30a(_)-TRC-OYE3_N194Y-lac-Icd).dna: Contain TRC-OYE3_N194Y and lac-Icd, for promoters evaluation
- pML43_(pET30a(_)-vector).dna: empty vector, for control experiments
- pML7_(pET30a(_)-T7-OYE3_N194Y-T7-GDH).dna: Contains the GDH gene, for NADPH regeneration
- pML70_(pET30a(_)-TRC-OYE3_N194Y-lac-GDH-no_tag).dna: Contain TRC-OYE3_N194Y and lac-GDH, for promoters evaluation
- pML71_(pET30a(_)-TRC-OYE3_N194Y-lac-Icd-no_tag).dna: Contain TRC-OYE3_N194Y and lac-Icd, for promoters evaluation
- pML8_(pET30a(_)-T7-OYE3_N194Y-T7-zwf).dna: Contains zwf gene, for NADPH regeneration
- pML81_(pET30a(_)-TRC-OYE1-lac-GDH).dna: Contain TRC-OYE1 and lac-GDH, for substrate scope
- pML82_(pET30a(_)-TRC-OYE1-lac-Icd).dna: Contain TRC-OYE1 and lac-Icd, for substrate scope
- pML83_(pET30a(_)-TRC-OYE1_H191A-lac-GDH).dna: Contain TRC-OYE1_H191A and lac-GDH, for substrate scope
- pML84_(pET30a(_)-TRC-OYE1_H191A-lac-Icd).dna: Contain TRC-OYE1_H191A and lac-Icd, for substrate scope
- pML85_(pET30a(_)-TRC-OYE1_Y82F-lac-GDH).dna: Contain TRC-OYE1_Y82F and lac-GDH, for substrate scope
- pML86_(pET30a(_)-TRC-OYE1_Y82F-lac-Icd).dna: Contain TRC-OYE1_Y82F and lac-Icd, for substrate scope
- pML89_(pET30a(_)-TRC-GluER_T36E_W66F_F68Y_P263L_F269Y_Q293T-lac-GDH).dna: Contain TRC-GluER_M6 and lac-GDH, for substrate scope
- pML9_(pET30a(_)-T7-OYE3_N194Y-T7-pos5).dna: Contain pos5 gene, for NADPH regeneration
- pML90_(pET30a(_)-TRC-GluER_T36E_W66F_F68Y_P263L_F269Y_Q293T-lac-Icd).dna: Contain TRC-GluER_M6 and lac-Icd, for substrate scope
- pYJ700_(pET30a(_)-OYE1-GDH).dna: Contains the n GDH gene, for NADPH regeneration
- pYJ702_(pET30a(_)-OYE1-Pos5).dna: Contain Pos5 gene, for NADPH regeneration
- pYJ727_(pET30a-Ptrc-PALY_RHOTO-PadA_LACPL-ppsA-tktA).dna: Contains 4-vinylphenol pathway genes, for 4-vinylphenol generation
- pYJ728_(pACYC_aroF-tyrA).dna: Contains 4-vinylphenol pathway genes, for 4-vinylphenol generation
- pYJ729_(pRSFDuet_Amp__Plac-tnaA).dna: Contain tnaA gene, for indole generation
- pYJ749_(4-vinylphenol_biosynthetic_genes_(pACYC-aroF-tyrA__Plac__T7p__PALY_RHOTO__PadA_LACPL__ppsA__tktA)).dna: Contain 4-vinylphenol pathway genes, for 4-vinylphenol generation
- pYJ750_(styrene_biosynthetic_genes_(pACYC-aroF-pheA__T7p__Ptrc__PAL2__FDC1__ppsA__tktA)).dna: Contain styrene biosynthetic genes, for styrene generation
- pYJ751_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori).dna: Contain 4-vinylphenol pathway genes, for 4-vinylphenol generation
- pYJ753_(pET30a-aroF-pheA__T7p__Ptrc__PAL2__FDC1__ppsA__tktA__pBR322_ori).dna: Contain styrene biosynthetic genes, for styrene generation
- pYJ755_(pACYC_vector__Chl__Plac-tnaA).dna: Contain tnaA gene, for indole generation
- pYJ761_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori__Trc-OYE3_N194Y__Lac-GDH).dna: Contain 4-vinylphenol and photoenzyme pathway genes, for photobiosynthesis fermentation
- pYJ762_(pET30a-aroF-tyrA__T7p__Ptrc__PALY_RHOTO__PadA_LACPL__ppsA__tktA__pBR322_ori__Trc-OYE3_N194Y__Lac-Icd).dna: Contain 4-vinylphenol and photoenzyme pathway genes, for photobiosynthesis fermentation
- pYJ763_(pRSF_ori__Trc-OYE3_N194Y__Lac-GDH).dna: Contain Trc-OYE3_N194Y and Lac-GDH, for photobiosynthesis fermentation
- pYJ764_(pRSF_ori__Trc-OYE3_N194Y__Lac-Icd).dna: Contain Trc-OYE3_N194Y and Lac-Icd, for photobiosynthesis fermentation
- pYJ767_(pRSF_ori__Trc-OYE1__Lac-GDH).dna: Contain Trc-OYE1 and Lac-GDH, for photobiosynthesis fermentation
- pYJ768_(pRSF_ori__Trc-OYE1_H191A__Lac-GDH).dna: Contain Trc-OYE1_H191A and Lac-GDH, for photobiosynthesis fermentation
- pYJ769_(pRSF_ori__Trc-OYE1_Y82F__Lac-GDH).dna: Contain Trc-OYE1_Y82F and Lac-GDH, for photobiosynthesis fermentation
- pYJ770_(pRSF_ori__Trc-GluER_M6__Lac-GDH).dna: Contain Trc-GluER_M6 and Lac-GDH, for photobiosynthesis fermentation
- pYJ771_(pRSF_ori__Trc-OYE1__Lac-Icd).dna: Contain Trc-OYE1 and Lac-Icd, for photobiosynthesis fermentation
- pYJ772_(pRSF_ori__Trc-OYE1_H191A__Lac-Icd).dna: Contain Trc-OYE1_H191A and Lac-Icd, for photobiosynthesis fermentation
- pYJ773_(pRSF_ori__Trc-OYE1_Y82F__Lac-Icd).dna: Contain Trc-OYE1_Y82F and Lac-Icd, for photobiosynthesis fermentation
- pYJ774_(pRSF_ori__Trc-GluER_M6__Lac-Icd).dna: Contain Trc-GluER_M6 and Lac-Icd, for photobiosynthesis fermentation
- pYJ775_(pRSF_ori__T7-OYE1-Y82G_T37Q).dna: Contain OYE1-Y82G_T37Q, for whole-cell mutants screening
- pYJ776_(pRSF_ori__T7-OYE1-WT).dna: Contain OYE1-WT, for whole-cell mutants screening
- pYJ777_(pRSF_ori__T7-OYE1-Y82G).dna: Contain OYE1-Y82G, for whole-cell mutants screening
- pYJ779_(pRSF_ori__T7-OYE1-Y82G_T37Q_W116A_H191S).dna: Contain OYE1-Y82G_T37Q_W116A_H191S, for whole-cell mutants screening
- pYJ783_(p15A_CmR-araBAD-TnaA).dna: Contains tnaA gene, for indole generation
- pYJ784_(pET30a(_)-T7-OYE3_N194Y-T7-GDH-ICD).dna: Contains GDH-ICD genes, for NADPH regeneration
- pYJ785_(pET30a(_)-T7-OYE3_N194Y-T7-Icd-GDH).dna: Contains Icd-GDH genes, for NADPH regeneration
- pYJ786_(pRSF_ori__Lac-GDH).dna: Contain Lac-GDH, without photoenzyme, for control experiments
- pYJ787_(pRSF_ori__Lac-Icd).dna: Contain Lac-Icd, without photoenzyme, for control experiments
