Bacterial strains, plasmids, and growth conditions
Strains used in this study are listed in Table 1. E. xiangfangensis were cultured in Luria-bertani medium (LB medium, per liter, 10 g of trypton, 5 g of yeast extract) at 30 ℃. E. coli strains were cultured in LB medium at 37 ℃.
Table 1
Bacterial strains and plasmids used in this work
Strain plasmid
|
Genotype, properties
|
Source or reference
|
Strain
E.Xiangfangensis
E.coli
|
Wild type
|
(Cao et al., 2018)
|
S17-1 (λpir)
|
TpR SmR recA, thi-1, pro, hsdR-M+RP4:2-Tc:Mu:Km Tn7 λpir
|
School of Pharmaceutical Science and Technology Tianjin University
|
Plasmid
|
|
|
pUC19
|
AmpR
|
School of Pharmaceutical Science and Technology Tianjin University
|
pRE112
|
Suicide vector,
CmR, SacB,oriT,oriV
|
School of Pharmaceutical Science and Technology Tianjin University
|
RNA-Seq library construction and sequencing
We selected the E. xiangfangensis strain as the key strain. After the activation, E. xiangfangensis were cultured in 5 mL LB medium at 30 ℃, 180 rpm for 24 hours until the light absorption value reached 0.5 at the wavelength of 600 nm. Then, 40 ng/L cis-verbenol was added to the final concentration as the treatment group, and DMSO was added to control.
The bacteria were cultured at 30 ℃, 180 rpm for another 16 hours and then were collected in a 1.5 mL tube by centrifugation at 12000 rpm for 3 min. Three replicates were conducted for each group. RNA extraction was performed using the RNeasy Mini Kit (QIAGEN, USA). RNA-Seq library construction and sequencing was completed by Beijing Novo Zhiyuan Sci-Tech Company Limited.
Transcriptome data analysis and synthetic pheromone related gene identification
Reads were mapped to the reference genome. The reference genome was completed by Beijing Novo Zhiyuan Sci-Tech Company Limited. Building of the reference genome index and alignment of clean reads to the reference genome were done using Bowtie2-2.2.3.
Because the pheromones of D. valens are synthesized by the oxidation process (Brand et al. 1975; Blomquist et al. 2010), the genes that belonged to oxidation-related gene families were selected for further analysis. Finally, pheromone-related genes were identified according to results from gene annotation. Based on these results, we chose ALDH as a target gene (see Results) for generating mutant strains without a functioning copy of this candidate gene potentially responsible for pheromone conversion.
Construction of the gene-deficient mutants
ALDH gene-deficient mutant strains of E. xiangfangensis were constructed using the homologous, double-cross-over method with the suicide vector pRE112 as previously described (Edwards et al. 1998; Yu et al. 2010; Deng et al. 2018).
Briefly, the upstream and downstream genomic sequences of the ALDH coding sequence were separately amplified using primers listed in Table 2. After ligating using restriction enzyme and digesting pRE112 using ClonExpress II One Step Cloning Kit (Vazyme, China) (Liu et al. 2020), the recombinant plasmid was transferred to the E.coli S17-1 (λpir) component cells. The positive clones were confirmed by PCR using primers in Table 2 and sequenced.
Table 2
Primers used in this work
Primer name
|
Primer sequence
|
Ex-ALDH1-up-F
|
CGACGGCCAGTGCCAAGCTTCGGTCATACCGAGCATCT
|
Ex-ALDH1-up-R
|
CGGCAAGAAAGAGGTGCGTTCTTCTCTCCAGATGTTTCGT
|
Ex-ALDH1-down-F
|
ACGAAACATCTGGAGAGAAGAACGCACCTCTTTCTTGCCG
|
Ex-ALDH1-down-R
|
ATGACCATGATTACGAATTCAGTAGTTACCGTCGCCCA
|
Ex-ALDH1-T1
|
GATCAGCGTCTTGCGGTA
|
Ex-ALDH1-T2
|
TTCCCATCGCAGACCTCA
|
Ex-ALDH1-T3
|
TTCTGCTCGAGATCCACCA
|
The positive E.coli S17-1 (λpir) colony was cultured in 5 mL LB medium at 37 ℃, 180 rpm for 16 hours, meanwhile the wild type E. xiangfangensis were cultured in 5 mL LB medium at 30 ℃, 180 rpm. Then, we mixed 1mL of each of the above two strains with 3 mL LB medium and cultured at 30℃, 180 rpm for 24 hours, after which the bacteria were collected and spread in the LB plate (50mg/L chloramphenicol, 50mg/L Ampicillin). After culturing overnight, the putative single-cross-mutant clones were confirmed by PCR, and cultured in LB medium for second-round homologous cross-over. The ALDH mutants were obtained by spreading the media in the LB agar plate containing 10% sucrose and confirmed by PCR with two pairs of primers.
Conversion experiments
Wild type E. xiangfangensis and its ALDH gene-deficient mutants were cultured in LB medium and incubated for 24 h. A dilution of 1:100 of each isolate was made when cultures were adjusted to an optical density (OD600).0.5. concentration (40 ng/µl and 200 ng/µl ) of cis-verbenol was then added into 4 ml bacterial suspensions and shaken for a further 36 h. Both the wild (control) and mutant E. xiangfangensis bacteria suspensions contained an equivalent amount of cis-verbenol. All solutions were extracted with hexane and then stored for later chemical analysis to determine verbenone concentration. The conversion experiments followed previously described methods (Cao et al. 2018), with slight modification of incubation and shaking times.
Statistical analysis
R software (version 3.0.3) was used to for pearson's correlation analysis, and significant correlations were declared at r > 0.8 or < −0.8. Conversion experiment results were analyzed using Dunnett’s T3 test, and significances were determined at P<0.05.