ABSTRACT
Aims@#The surplus use of herbicide Dalapon® contains 2,2-dichloropropionic acid (2,2-DCP) poses great danger to human and ecosystem due to its toxicity. Hence, this study focused on the isolation and characterization of a dehalogenase producing bacteria from Sungai Skudai, Johor, capable of utilizing 2,2-DCP as a carbon source and in silico analysis of its putative dehalogenase.@*Methodology and results@#Isolation of the target bacteria was done by using 2,2-DCP-enriched culture as the sole carbon source that allows a bacterium to grow in 20 mM of 2,2-DCP at 30 °C with the corresponding doubling time of 8.89 ± 0.03 h. The isolated bacterium was then designated as Klebsiella pneumoniae strain YZ based on biochemical tests and basic morphological examination. The full genome of K. pneumoniae strain KLPN_25 (accession number: RRE04903) which obtained from NCBI database was screened for the presence of dehalogenase gene, assuming both strains YZ and KLPN_25 were the same organisms. A putative dehalogenase gene was then identified as type II dehalogenase from the genome sequence of strain KLPN_25. The protein structure of the type II dehalogenase of KLPN_25 strain was then pairwise aligned with the crystal structure of L-2-haloacid dehalogenase (L-DEX) Pseudomonas sp. strain YL as the template, revealing the existence of conserved amino acids residues, uniquely known to participate in the dehalogenation mechanism. The finding thus implies that the amino acid residues of type II dehalogenase possibly shares similar catalytic functions with the L-DEX.@*Conclusion, significance and impact of the study@#In conclusion, this study confirmed the presence of new dehalogenase from the genus Klebsiella with potential to degrade 2,2-DCP from the river water. The structural information of type II dehalogenase provides insights for future work in designing haloacid dehalogenases.
Subject(s)
Computer Simulation , Molecular Dynamics SimulationABSTRACT
Aims@#The use of herbicide effectively controls weeds in agricultural practice. However, its release to the surrounding surface water bodies may lead to environmental issues. The aim of this study was to isolate the bacteria that were able to remove 2,2-dichloropropionic acid (2,2-DCP) from a paddy field located in Malang. @*Methodology and results@#The 2,2-DCP degrading bacteria were isolated and their ability to grow on higher 2,2-DCP concentrations (50 and 80 mM) was tested. Bacterial degradation of 2,2-DCP was examined through measurement of released chloride ions. The potential isolates were identified according to their 16S rDNA sequences. Two potential isolates, BB9.2 and BC14.3 were observed for their growth on 20, 50, and 80 mM 2,2-DCP. Isolate BC14.3 had the shortest cell doubling time of approximately 4.1 h with 100% 2,2-DCP (20 mM) utilization, whereas BB9.2 was only able to degrade 80% of 2,2-DCP at the same concentration. The 16S rDNA gene sequences suggested that BB9.2 and BC14.3 belong to Acinetobacter calcoaceticus and Pseudomonas plecoglossicida, respectively. @*Conclusion, significance and impact of study@#Bacterial strains with 2,2-DCP degrading potentials were successfully isolated from long-term exposed agricultural soil. They demonstrated notable utilization of the organic halide. This is the first time that strains of A. calcoaceticus and P. plecoglossicida were reported to utilize 2,2-DCP.