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8 protocols using jm109

1

Strains and Growth Conditions for Studying Ustilago

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The Escherichia coli strain JM109 (Takara) was used for cloning purposes. The compatible haploid T type strains UeT14 (a1b1 CCTCC AF 2015016) and UeT55 (a2b2 CCTCC AF 2015015) and their derivatives (listed in Supplementary Table S1) were used in this study. The strains of U. maydis used in this study are also listed in Supplementary Table S1. The growth conditions and media for E. coli (Russell and Sambrook, 2001 ), U. maydis (Holliday, 1974 ), and U. esculenta (Zhang et al., 2019 (link)) have previously been described. The growth conditions of Zea mays (the early golden bantam) and the wild Z. latifolia used for pathogenic development assays of tested strains before and after stem injection have previously been described (Flor-Parra et al., 2007 (link); Zhang et al., 2019 (link)).
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2

miRNA Expression Profile in Rhipicephalus microplus

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In this study, R. microplus ticks were collected from Yongjing County, Gansu Province, and maintained under laboratory conditions. These ticks were identified using morphology by the Animal Research Institute (Lanzhou Veterinary Research Institute). Approximately 0.5 mg of eggs and 1 g of larvae were used for miRNA extraction, and another 1 g of larvae was placed in a cloth bag attached to cattle for 25 ± 3 days to produce engorged adult female ticks. To analyze the expression profile of miRNAs in R. microplus, unfed larvae, adult female ticks and eggs were ground in liquid nitrogen to extract total RNA using TRIzol reagent (Invitrogen, Cat No. 15596-026). The concentration of RNA was 400 ng/mL (260/280 = 2.00). Some RNAs were used to construct libraries for small RNA sequencing, and some were used for miRNA validation. The synthesis of first-strand cDNAs was performed according to the protocol for transcriptase XL (Avian Myeloblastosis Virus, AMV) (TaKaRa, Shiga, Japan) with a loop primer of miRNAs and oligo dT18. PCR was performed to obtain the miRNAs sequence. The PCR product was ligated to the T-Easy vector (TaKaRa, Japan), which was transformed into JM109 (TaKaRa, Japan). The sequence was obtained by GenScript (Nanjing, China).
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3

Characterization of Ambergris Volatiles using GC-MS

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E. coli JM109 (Takara, Shiga, Japan) was used for sequencing analysis, and E. coli BL21(DE3) (Takara), pColdTF (Takara), and pColdI (Takara) were used to express BmeTCX genes. NMR spectra were recorded using a Bruker DPX 400 spectrometer (Billerica, MA, USA) at 400 MHz for protons (1H) and 100 MHz for carbon (13C). GC–MS was performed on a JMS-T100GCV spectrometer (JEOL, Tokyo, Japan) equipped with a DB-1 capillary column (30 m × 0.25 mm × 0.25 µm; J&W Scientific. Inc., Folsom, CA, USA), using the EI mode operated at 70 eV. GC analyses were performed using a Shimadzu GC-2014 chromatograph equipped with a flame ionization detector and using a DB-1 capillary column (30 m × 0.25 mm × 0.25 µm; J&W Scientific, Inc.). GC and GC–MS conditions for the BmeTCX products were as follows: injection temperature = 300 °C, column temperature = 220–300 °C (1 °C min−1). GC and GC–MS conditions for the volatile compounds were as follows: injection temperature = 200 °C, column temperature = 40–300 °C (5 °C min−1) for GC and 30–300 °C (5 °C min-1) for GC–MS. Compound 6 was purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). Two ambergris samples (NSMT M55020 and NSMT M55019; Supplementary Fig. 7) stored in the National Museum of Nature and Science (Japan) for more than 30 years were used for the analysis of volatile components.
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4

Escherichia coli Cloning and Protein Expression

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The Escherichia coli strain JM109 (TaKaRa, Shiga, Japan) was used for cloning plasmid DNA. The E. coli strain C41 (DE3) (Cosmo Bio, Tokyo, Japan) harboring biliverdin (BV) synthetic system, pKT270, was used for protein expression as previously reported [24 (link),35 (link)]. Bacterial cells were grown in Lysogeny Broth (LB) medium containing 20 µg/mL kanamycin with or without 20 µg/mL chloramphenicol.
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5

Bacterial Cloning and Co-expression System

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The Escherichia coli strain JM109 (TaKaRa) was used for plasmid DNA cloning. The E. coli strain C41 (Cosmo Bio) harboring plasmid pKT271 (constructed by heme oxygenase and phycocyanobilin:ferredoxin oxidoreductase genes from Synechocystis sp. PCC 6803) (Mukougawa et al. 2006 ) was used for co-expression of proteins with the PCB-producing system. Bacterial cells were grown on lysogeny broth (LB) agar medium containing 20 µg/mL kanamycin with or without 20 µg/mL chloramphenicol for selection of plasmid-transformed cells.
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6

E. coli and Yeast Strain Cultivation

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The E. coli strains used in this study were JM109 (Takara Bio Inc., Shiga, Japan) and BL21(DE3) (Novagen, Abingdon, UK), which were grown in Luria-Bertani (LB) medium (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) with aeration at 37 °C. Saccharomyces cerevisiae OP-3C was as described previously. 21 Plasmid pET-42b was from Novagen. Inorganic pyrophosphatase, purine nucleoside phosphorylase, xanthine oxidase and horseradish peroxidase were purchased from Sigma-Aldrich. Potato acid phosphatase was purchased from GE Healthcare UK Ltd. (Buckinghamshire, UK). Restriction enzymes and other DNA-modifying enzymes were purchased from New England Biolabs (Beverly, MA, USA) or Takara Bio Inc. and used as described by the manufacturers.
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7

Plasmid Transformation in E. coli

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Escherichia coli strain JM109 (Takara, Japan) was used for the transformation of high-copy plasmids. Transformation of highcopy plasmids was carried out by a heat-shock protocol using chemically treated competent cells according to the manufacturer's instruction. For transformation of low-copy bacmids, E. coli strain DH10b (Invitrogen, USA) was used. Low-copy bacmids were transformed into electrocompetent cells by electroporation as follows. Competent cells (200 µl) were mixed with 1 µg of bacmid DNA and single shocked in a 0.1 cm electroporation cuvette (Bio-Rad, USA) using a Bio-Rad Gene Pulser under the following conditions: volts, 1.8 kV; resistance, 200 Ω; and capacitance, 25 µF. All of the restriction endonucleases and modifying enzymes were from Roche Applied Science (Germany).
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8

Engineered CYP53A15 for Bacterial Expression

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CYP53A15 cDNA with two nucleotide substitutions (G105C and C107G) and six additional nucleotides was artificially synthesized by GeneArt Gene Synthesis (Thermo Fisher Scientific, USA), and obtained as a pMK-RQ-CYP53A15 plasmid; these nucleotide modifications add SmaI (CCCGGG) and SalI (GTCGAC) recognition sites (Fig. 1A). The pMK-RQ-CYP53A15 plasmid was digested with SmaI and SalI and ligated into five modified pCWR vectors for coexpression of P450 and CPR (Fig. 1B). These five modified pCWR vectors each contain one of various DNA sequences encoding N-terminal peptides of mammalian P450s at the start codon, as follows: pCWRm1A2N (MALLLAVFLFCLVFWMVR ASRTQVPKGLKNPPG); pCWRrab2C3N (MAKKTSSKGKLPPG); pCWRr2C11N (MARQSFGRGKLPPG); pCWRm2C29N (MARQSS GRGKLPPG); and pCWRh2E1N (MARQVHSSWNLPPG) (Fig. 1C). The resulting plasmids were introduced into E. coli strains JM109 and BL21(DE3) (Takara, Japan), and BW25113, ΔgcvR, ΔcpxA, and ΔglnL, which were obtained from the National BioResource Project-E. coli (NBRP-E. coli) at the National Institute of Genetics (Japan).
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