Genomic and transcriptomic analyses of the haloacid-degrading Burkholderia caribensis MBA4

Abstract

Burkholderia caribensis MBA4 was studied for its capability to degrade and utilize haloacids as sole carbon and energy source. An operon containing a dehalogenase deh4a and a transporter deh4p was responsible for dehalogenation and haloacid uptake. To understand the utilization of haloacid in MBA4, a proteomic analysis of the degradation of chloroacetate had been performed. However, the identities of most of the differentially expressed proteins were unknown because of the lack of a complete genome sequence. Furthermore, in order to reveal the global gene expression patterns of the bacterium during remediation of haloacid it was necessary to adopt more sensitive method such as RNA-seq analysis. In this study, sequencing reads of MBA4 obtained from Illumina, Roche454 and PacBio platforms were de novo assembled into a complete genome. The total size of the genome is 9,482,704 bp with a GC content of 62.46 %. It consists of three replicons encoding 9,056 protein-coding and 80 RNA genes. The genome was compared with that of twelve phylogenetically related strains. The results indicated that MBA4 has remarkable evolutionary capacity as it possesses many tandem repeats, mobile genetic elements, and genomic islands. Besides, most key genes involved in haloacid utilization were unique to MBA4. These genes were clustered in a special chromosomal region that maybe acquired from a plasmid by horizontal gene transfer. Transcriptomic profiling of cells grown on 2-carbon monochloroacetate and glycolate, and 3-carbon 2-bromopropionate and lactate were determined. The profile of cells grown on pyruvate was used as a control. Comparative results showed that 2-bromopropionate induced more and repressed fewer genes than monochloroacetate. 2-Bromopropionate up regulated 236 genes while down regulated 199 genes. For monochloroacetate, 81 genes were induced while 346 genes were repressed. Genes grouped with deh4a and deh4p in hierarchical clustering were considered to be key genes involved in haloacid degradation. There were 48 and 34 genes being identified in response to degradation of monochloroacetate and 2-bromopropionate, respectively. Among these genes, nine of them were found to be induced by both monochloroacetate and 2-bromopropionate. These genes included deh4a, deh4p, a TetR regulator, a LysR regulator, a putative hydrolase or acyltransferase, a dehydropantoate reductase, an L-alanine-DL-glutamate epimerase, a permease of the drug/metabolite transporter superfamily and a permease of the major facilitator superfamily. These genes were believed to play essential roles in MBA4 in utilization of haloacid and halopropionate.