RNA-seq analysis of the degradation of chloroacetate by Burkholderia caribensis MBA4. Paraburkholderia caribensis

Burkholderia caribensis MBA4 is able to metabolize monochloroacetate (MCA) as sole carbon and energy source for growth. A haloacid dehalogenase is mainly responsible for the cleavage of the carbon-halogen bond. The MCA will be hydrolyzed to glycolate which would be further transformed to glyoxylate by glycolate oxidase. In order to identify inducible genes involved in mineralization of MCA, transcriptomes of MBA4 cells grown on MCA, glycolate or pyruvate were determined using RNA-seq technology. After trimming and filtering, clean data of each transcriptome were mapped to an annotated genome of MBA4 and the expression values of various genes were calculated and compared. The results showed that there are specific sets of genes being induced by MCA and not by its dehalogenation product glycolate. Noticeably, among three glycolate oxidase operons identified in the genome their expressions were found to be varied individually in response to MCA, glycolate and pyruvate. One of the operons was minimally expressed no matter what was the growth substrate. Another operon was inducible both by MCA and glycolate. This is expected and which suggested that this operon is most likely responds to the presence of glycolate. The third operon contains the structural genes, glcDEF, for glycolate oxidase, glcG, for an uncharacterized protein associated with glycolate metabolism, and glcB, for malate synthase G. This operon was inducible by MCA only and not by glycolate nor pyruvate. Overall design: RNA-seq data obtained from pyruvate-, glycolate- or monochloroacetate-grown cells of a Burkholderia caribensis were analyzed and compared.