Comparison of thioesterase Ynep in Bacillus nematocida B16 and Bacillus subtilis 168

Abstract:

[Background]The biocontrol bacteria Bacillus nematicida B16 and B. subtilis 168 present different perceptions for nematodes and have significant differences in the expression of the nematode attractant 2-heptanone.[Objective] To investigate the key factor, the thioesterase Ynep, involved in methyl ketone synthesis in B. nematicida B16 and B. subtilis 168, and compare the heterologous expression, structure, and activity of this enzyme between the two strains. [Methods] Quantitative polymerase chain reaction (qPCR) was employed to examine the transcriptional levels of thioesterase in the two Bacillus strains. Bioinformatics analysis was conducted to compare the structural differences of this enzyme. Furthermore, the heterologous expression level and activity of this protein were compared between the two strains. [Results] The transcription level of ynep in B. nematicida B16 was 1.428 and 0.991 folds of that in B. subtilis 168 at the time points of 12and 72 h, respectively. Bioinformatics analysis indicated an amino acid sequence identity of 97.12% between the two enzymes. The two enzymes were predicted to have the molecular weights of 15 993.35 Da and 16 007.42 Da and the isoelectric point (pI) values of 7.06 and 7.82, respectively. They possessed the transcriptional enhancer (TE) domain with the conserved catalytic triad Asp16-His23-Tyr26. Homology modeling revealed that both Ynep enzymes presented the typical "hot dog" fold, a common structure in the TE superfamily. Four residue differences existed between the two enzymes, potentially influencing the formation of the thioesterase tetramer. The Ynep in B. nematicida B16 and B. subtilis 168 showed the binding energy of -5.47 kcal/mol and -6.95 kcal/mol, respectively, with the substrate β-ketoacyl-CoA. The purified recombinant enzymes of B. nematicida B16 and B. subtilis 168 demonstrated the activities of 1.243 U/mL and 1.233 9 U/mL, respectively. Both enzymes exhibited optimal reaction temperatures of 30 and optimal pH 8.0 and 9.0, respectively. Both enzymes demonstrated good stability within the temperature range from 10 to 30 and at pH 7.0-8.0. Moreover, the Ynep in B. subtilis 168 had stronger thermal tolerance than that in B. nematicida B16. [Conclusion] The thioesterase Ynep in the two Bacillus strains shows differences in heterologous expression, structure, and enzyme activity, which lead to variations in the synthesis of 2-heptanone. The findings contribute to the understanding of the molecular mechanisms underlying the different perceptions of nematodes by different Bacillus strains, providing new insights for the development of efficient biocontrol products against nematodes.