Generation of structurally novel short carotenoids and study of their. biological activity
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1 Supplementary Information Generation of structurally novel short carotenoids and study of their biological activity Se H. Kim 1, Moon S. Kim 2, Bun Y. Lee 2 & Pyung C. Lee 2,* 1 The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kogle Alle 6, 2970 Hørsholm, Denmark 2 Department of Molecular Science and Technology and Department of Applied Chemistry and Biological Engineering, Ajou University, Woncheon-dong, Yeongtong-gu, Suwon , South Korea * Address correspondence to Pyung Cheon Lee pclee@ajou.ac.kr, Tel: , Fax: Table S1. Bacterial strains and plasmids used in this study Source or Strains and plasmids Relevant properties reference Strains Nostoc sp. PCC 7120 C 40 carotenogenic pathway UTEX 2576 enda1 glnv44 thi-1 gyra96 rela1 lac recb recj sbcc Escherichia coli str. SURE umuc::tn5 uvrc e14- Δ(mcrCB-hsdSMR-mrr)171 Stratagene F'[ proab + laci q laczδm15 Tn10] Escherichia coli str. XL1-Blue enda1 gyra96(nal R ) thi-1 reca1 rela1 lac glnv44 F'[::Tn10 proab + laci q - Δ(lacZ)M15] hsdr17(r K m K+ ) Stratagene
2 Pantoea agglomerans KCTC 2479 C 40 zeaxanthin diglucoside biosynthesis pathway KCTC Rhodobacter capsulatus KCTC 2583 C 40 spheroidenone biosynthesis pathway KCTC Corynebacterium glutamicum KCTC 1445 C 50 decaprenoxanthin diglucoside biosynthesis pathway KCTC Salinibacter ruber DSMZ C 40 carotenoid biosynthesis pathway DSMZ Plasmids pucm Cloning vector modified from puc19. Constitutive lac promoter, Ap 1 pbbr1mcs-2 Cloning vector. SC101 origin. Inducible lac promoter, 2 Km R pacyc184 Expression vector that is compatible with pmb1 or ColE1 related plasmids NEB pucm-y BL Constitutively expressed crtycyd from B. linens 1 pucm-y tbl Constitutively expressed crtycyd mutant genes pucm-y PA Constitutively expressed crty from P. agglomerans 3 pucm-y PN Constitutively expressed crty from P. ananatis 1 pucm-y SR Constitutively expressed crty from S. ruber pucm-z PA Constitutively expressed crtz from P. agglomerans 3 pucm-x PA Constitutively expressed crtx from P. agglomerans pucm-m SA Constitutively expressed crtm from S. aureus 4 pucm-n SA Constitutively expressed crtn from S. aureus 4 pucm-n rsa Constitutively expressed crtn r mutant pucm-n ysa Constitutively expressed crtn y mutant pucm-n zsa Constitutively expressed crtn z mutant pucm-a RC Constitutively expressed crta from Rhodobacter capsulatus 1 pucm-d RC Constitutively expressed crtd from Rhodobacter capsulatus pucm-eb CG Constitutively expressed crteb from Corynebacterium glutamicum pucm-y CG Constitutively expressed crtyeyf from Corynebacterium glutamicum pucm-o SY Constitutively expressed crto from Synechocystis sp. PCC pucm-w NO Constitutively expressed crtw from Nostoc sp. PCC pbbr-aldh SA Inducibly expressed aldh from S. aureus 4
3 pacm-m SA-N SA pacm-m SA-N ysa pacm-m SA-N zsa pacm-m SA-N SA-P SA pacm-m SA-N ysa-y tbl pacm-m SA-N zsa-y PA pacm-m SA-N ysa-y tbl-z PA pacm-m SA-N zsa-y PA-Z PA Constitutively expressed crtm, and crtn from S. aureus to produce 4,4 -diapolycopene Constitutively expressed crtm, and crtn y from S. aureus to produce 4,4 -diaponeurosporene Constitutively expressed crtm, and crtn z genes from S. aureus to produce 4,4 -diapo-ζ-carotene Constitutively expressed crtm, crtn and crtp genes from S. aureus to produce 4,4 -diaponeurosporen-4 -al Constitutively expressed crtm, crtn y and crty t genes from S. aureus and B. linens to produce 4,4 -diapotorulene Constitutively expressed crtm, crtn z, and crty genes from S. aureus and P. agglomerans to produce 4,4 -diapo-βcarotene Constitutively expressed crtm, crtn y crty t, and crtz genes from S. aureus, B. linens and P. agglomerans to produce 7-hydroxy-4,4 -diapotorulene Constitutively expressed crtm, crtn z, crty, and crtz genes from S. aureus and P. agglomerans to produce 4,4 -diapoβ-cryptoxanthin 4
4 Table S2. Primers used in this study Gene Sequence Enzyme site crtd RC F:5 GCTCTAGAAGGAGGATTACAAAATGCGGAGTGAAACGGAC 3 XbaI R:5 CTGGCGATATCCTACTTCGCGGCGGAAATC 3 EcoRV crteb CG F:5 GCTCTAGAAGGAGGATTACAAAATGATGGAAAAAATAAGACTA 3 XbaI R:5 GGAATTCTTATATCTGATGAATTGCTAT 3 EcoRI crty CG F:5 GCTCTAGAAGGAGGATTACAAAATGATCCCTATCATCGATAT 3 XbaI R:5 GGAATTCCTACGGCTTTTCTGGCTC 3 EcoRI crty SR F:5 GCTCTAGAAGGAGGATTACAAAATGAGCTATCTATCTTTCCATC 3 XbaI R:5 GGAATTCTTAGGTCGCGGACAGG 3 EcoRI crtx PA F:5 GCTCTAGAAGGAGGATTACAAAATGAGCCACTTTGCGGTC 3 EcoRI R:5 CCGGAATTCTCATACCGCGGCATAGTG 3 NotI Sub_HindIII_F F:5 CCCAAGCTTCCGACTGGAAAGCG 3 HindIII Sub_HindIII_R R:5 CCCAAGCTTCGGTGTGAAATACCG 3 HindIII Sub_BamHI_F F:5 CGGGATCCCCGACTGGAAAGCG 3 BamHI Sub_BamHI_R R:5 CGGGATCCCGGTGTGAAATACCG 3 BamHI Sub_SalI_F F:5 ACGCGTCGACCCGACTGGAAAGCG 3 SalI Sub_SalI_R R:5 ACGCGTCGACCGGTGTGAAATACCG 3 SalI Sub_PpuMI_F F:5 ACGAGGACCCCCGACTGGAAAGCG 3 PpuMI Sub_PpuMI_R R:5 ACGAGGACCCCGGTGTGAAATACCG 3 PpuMI crtn A134V F:5 TAAAAAATATGAAATTGTACGTCGCTATTTCTTAG 3 R:5 CTAAGAAATAGCGACGTACAATTTCATATTTTTTA 3 crtn E246G F:5 ACTTAATGCTGAAATTGGGCAAATTATTATTGATC 3 R:5 GATCAATAATAATTTGCCCAATTTCAGCATTAAGT 3 crtn M58T F:5 CCCCACAATTGTCATGACGCCAGATGTTTATAAAG 3 R:5 CTTTATAAACATCTGGCGTCATGACAATTGTGGGG 3 crtn F443L F:5 CGAAATTTGGTTCGGCACTCGGTTTAATGCCAACT 3 R:5 AGTTGGCATTAAACCGAGTGCCGAACCAAATTTCG 3 crtn E209G F:5 AATTATTCCTATGATTGGAATGATGTTTGGTGTGC 3 R:5 GCACACCAAACATCATTCCAATCATAGGAATAATT 3 crtn N232S F:5 AGGGCTAGCGCAATTAAGTAAAGATTTAGGCGTTA 3 R:5 TAACGCCTAAATCTTTACTTAATTGCGCTAGCCCT 3 crtn F212S F:5 TATGATTGAAATGATGTCTGGTGTGCATTTTATTA 3 R:5 TAATAAAATGCACACCAGACATCATTTCAATCATA 3 crtn D350G F:5 AGGGCGATTATCGCATGGTCCTTCTATTTATGTGT 3 R:5 ACACATAAATAGAAGGACCATGCGATAATCGCCCT 3
5 Table S3. Nucleotide and amino acid changes in selected mutant clones Nucleotide Codon usage Amino acid CrtNwt CrtNr04 C401T (GCA GTA) A737G (GAG GGG) A134V E246G CrtNr07 A75G (GAA GAG) A626G (GAA GGA) A695G (AAT AGT) E209G N232S CrtNy02 T635C (TTT TCT) T840C (AGT AGC) A1049G (GAT GGT) F212S - D350G CrtNy08 A185G (TAT TGT) T367C (TTT CTT) T578G (ATT AGT) A627G (GAA GAG) A1046G (CAT CGT) Y62C F123L I193S - H348R CrtNy11 T173C (ATG ACG) T1327C (TTC CTC) T1458C (AGT AGC) M58T F443L -
6 Figure S1. Carotenoid profiles of CrtN mutants. E. coli expressing background pacm- MSA were transformed with each mutant clone, including mutants generated by site-directed mutagenesis and those cultivated for 48 h in TB medium. Carotenoids were identified as follows: 1. 4,4-diapolycopene, and 2. 4,4-diaponeurosporene.
7 Figure S2. Carotenoid profiles of screened CrtYBL mutants. E. coli expressing background pacm-msa-nsa were transformed with each mutant clones and cultivated for 48 h in TB medium. Representative cell pellets and identified carotenoid structures are shown in the right panel.
8 Figure S3. 1 H NMR spectrum of 4,4 -diapotorulene and its assignment. (The signals marked with "*" are from C6D6 and the eluent residue) 1 H NMR (600 MHz, C6D6): δ 6.76 (dd, J = 16, 11 Hz, 1H), 6.72, 6.70, 6.68, and 6.66 (AA'BB', 2H), 6.64 (dd, J = 16, 11 Hz, 1H), 6.49 (d, J = 16 Hz, 1H), 6.42 (d, J = 16 Hz, 1H), (d, J = 19 Hz, 1H), (d, J = 11 Hz, 1H), (d, J = 19 Hz, 1H), 6.35, 6.33, 6.31, and 6.29 (AA'BB', 2H), 6.07 (d, J = 11 Hz, 1H), 1.98 (m, 2H), 1.92 (s, 3H), 1.90 (s, 3H), 1.86 (s, 3H), 1.83 (s, 3H), 1.71 (s, 3H), 1.68 (s, 3H), 1.60 (m, 2H), 1.50 (m, 2H), 1.16 (s, 6H) ppm.
9 Figure S4. Mass spectra of carotenoids produced by engineered E. coli cells in this study. Mass spectra were recorded using both negative and positive APCI ion source as indicated in Materials and Methods.
10 Figure S5. rbmsc viability after treatment with varying concentrations of 4,4 - diapotorulene for 7 days. Cells were treated with varying concentrations of 4,4 - diapotorulene, and the viability of the treated cells was measured with an MTT assay. Values are expressed as means ± SD and each experiment was performed in triplicate, (*p < 0.001).
11 Figure S6. Selected C40 and C50 carotenoid biosynthesis pathway enzymes in nature. Enzymes represented in boldface were used for creating and extending structurally novel C30 and C35 carotenoids including acyclic, monocyclic, and bicyclic structures. Red circles indicate specific functional groups catalyzed by corresponding C40 or C50 carotenoidmodifying enzymes. Idi (IPP isomerase), IspA (FPP synthase), CrtE (GGPP synthase), CrtB (phytoene synthase), CrtI (phytoene desaturase), CrtY (lycopene cyclase), CrtZ (β-carotene hydrolase), CrtX (zeaxanthin glucosyltransferase), CrtW (β-carotene ketolase), CrtO (carotene ketolase), CrtEb (lycopene elongase), CrtD (1-hydroxycarotenoid 3,4-desaturase), and CrtA (spheroidene monooxygenase).
12 Supplementary References 1. Kim, S.H., Park, Y.H., Schmidt-Dannert, C. & Lee, P.C. Redesign, Reconstruction, and Directed Extension of the Brevibacterium linens C 40 Carotenoid Pathway in Escherichia coli. Appl. Environ. Microbiol. 76, (2010). 2. Kovach, M.E. et al. Four new derivatives of the broad-host-range cloning vector pbbr1mcs, carrying different antibiotic-resistance cassettes. Gene 166, (1995). 3. Song, G.H., Kim, S.H., Choi, B.H., Han, S.J. & Lee, P.C. Heterologous carotenoid-biosynthetic enzymes: Functional complementation and effects on carotenoid profiles in Escherichia coli. Appl. Environ. Microbiol. 79, (2013). 4. Kim, S.H. & Lee, P.C. Functional expression and extension of staphylococcal staphyloxanthin biosynthetic pathway in Escherichia coli. J. Biol. Chem. 287, (2012). 5. Lee, P.C., Momen A.Z.R., Mijtz B.N. & Schmidt-Dannert, C. Biosynthesis of structurally novel carotenoids in Escherichia coli. Chem. Biol. 10, (2003). 6. Kim, S.H., Kim, J.H., Lee, B.Y. & Lee, P.C. The astaxanthin dideoxyglycoside biosynthesis pathway in Sphingomonas sp. PB304. Appl. Microbiol. Biotechnol. 98, (2014).
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