Complete genome sequence of Acinetobacter indicus and identification of the hydrolases provides direct insights into phthalate ester degradation

Abstract

A strain designated Acinetobacter indicus WMB-7 with the ability to hydrolyze phthalate esters (PAEs) was isolated from the fermented grains of Baijiu. The genome of the strain was sequenced with a length of 3,256,420 bp and annotated with 3183 genes, of which 36 hydrolases encoding genes were identified. The hydrolases were analyzed by protein structure modeling and molecular docking, and 14 enzymes were docked to the ligand di-butyl phthalate with the catalytic active regions, and showed binding affinity. The 14 enzymes were expressed in E. coli and 5 of them showed the ability for PAEs hydrolysis. Enzyme GK020_RS15665 showed high efficiency for PAEs hydrolysis and could efficiently hydrolyze di-butyl phthalate under an initial concentration of 1000 mg/L with a half-life of 4.24 h. This work combined a series of methods for identifying PAEs hydrolases and offered a molecular basis for PAEs degradation of A. indicus strains from Baijiu.

Supplementary information: The online version contains supplementary material available at 10.1007/s10068-023-01334-w.

Keywords: Acinetobacter indicus; Baijiu; Ester bond hydrolysis; Molecular docking; Phthalate esters.

Fig. 1

Circular map of A. indicus WMB-7 based on genome sequence and annotation. From outside to inside: forward strand gene, reverse strand gene, forward strand RNAs, reverse strand RNAs, repeat, GC content, GC skew

Fig. 2

Protein structure modeling of the potential PAEs hydrolases and molecular docking to DBP. (A) GK020_RS11185; (B) GK020_RS11230; (C) GK020_RS15275; (D) GK020_RS15155; (E) GK020_RS03995; (F) GK020_RS15665; (G) GK020_RS05500; (H) GK020_RS09115; (I) GK020_RS10440; (J) GK020_RS07540; (K) GK020_RS08875; (L) GK020_RS08850; (M) GK020_RS05280; (N) GK020_RS06805

Fig. 3

PCR amplification of the genes (A) and SDS-PAGE analysis of the enzymes (B) with molecular docking interactions to DBP. M, marker; NC, negative control

Fig. 4

Verification of the PAE-degrading ability of the enzymes (A) and degradation efficiency of the enzyme GK020_RS15665 (B). All experiments were carried out in triplicate. NC, negative control, the crude enzyme solution of E. coli BL21/pET-28a(+)