Proteomic study of linuron and 3,4-dichloroaniline degradation by Variovorax sp. WDL1: evidence for the involvement of an aniline dioxygenase-related multicomponent protein

A proteomic approach was used to explore the metabolism of the phenylurea herbicide linuron and 3,4-dichloroaniline (3,4-DCA) in Variovorax sp. WDL1. This bacterium grows on linuron as sole source of carbon, nitrogen and energy, while it transiently accumulates 3,4-DCA as a metabolite. Differential protein expression analysis of Variovorax sp. WDL1 grown in a heterotrophic medium in the presence and absence of linuron or 3,4-DCA was conducted using 2-D PAGE. Selected up- and downregulated proteins were identified with nanoLC-ESI-MS/MS. In the 3,4-DCA-supplemented culture, upregulation of several proteins showing high amino acid sequence similarity to different components of the multicomponent aniline dioxygenase in aniline-degrading Proteobacteria was observed. For one of the components, multiple variant proteins were detected, suggesting that strain WDL1 harbors several copies of the aniline dioxygenase (AD) gene cluster which are simultaneously expressed in the presence of 3,4-DCA. A number of unidentifiable proteins, which were upregulated in the linuron- and/or 3,4-DCA-supplemented cultures, might represent up to now uncharacterized proteins with a role in linuron and/or 3,4-DCA degradation in strain WDL1. In addition, several stress-related proteins were differentially expressed.