RNA-Seq analysis of the degradation of haloacetate by Burkholderia caribensis MBA4

Abstract

Burkholderia caribensis strain MBA4 was isolated for its ability to utilize monobromoacetate as carbon and energy source. This bacterium produced an inducible haloacid dehalogenase that transforms monohaloacetate to glycolate and to glyoxylate by glycolate oxidase. Genomic analysis of the bacterium showed that it contains three glycolate oxidases: ETY79679-81, ETY80271-3 and ETY84258-60. Transcriptomic analysis showed that ETY79679-81 was expressed constitutively to a reads per kilobase transcript per million reads (RPKM) value of around 100 no matter the substrate was pyruvate, glycolate or chloroacetate. ETY80271-3 gave values of 7 in pyruvate-, 867 in chloroacetate- and 1260 in glycolate-grown cells. ETY84258-60 gave values of 20 in pyruvate-, 1880 in chloroacetate- and 178 in glycolate-grown cells. A malate synthase G gene, ETY84261, was found downstream of ETY84258-60. Apparently, ETY80271-3 converted glycolate to glyoxylate and through the glycerate pathway to pyruvate. When MBA4 was grown on chloroacetate, gene products of ETY84258-61 were mainly used and malate was generated. Putative regulator GlcC genes, ETY80275 and ETY84257, can be found upstream of ETY80271-3 and ETY84258-60, respectively. The expression profiles of these glycolate oxidases suggested that both GlcC were activated by glycolate and chloroacetate with ETY80275 more responsive to glycolate and ETY84257 more reactive towards chloroacetate. While the relative transcript levels of ETY80275 were rather stable, expression of ETY84257 was enhanced in glycolate- and even more in chloroacetate-grown cells. The characterization of the degradation of haloacetate by B. caribensis MBA4 is made possible with the use of RNA-seq analysis.