Abstract
BackgroundThe genus Burkholderia includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND) family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. This study aims to i) identify rnd genes in the 21 available completely sequenced Burkholderia genomes, ii) analyze their phylogenetic distribution, iii) define the putative function(s) that RND proteins perform within the Burkholderia genus and iv) try tracing the evolutionary history of some of these genes in Burkholderia.ResultsBLAST analysis of the 21 Burkholderia sequenced genomes, using experimentally characterized ceoB sequence (one of the RND family counterpart in the genus Burkholderia) as probe, allowed the assembly of a dataset comprising 254 putative RND proteins. An extensive phylogenetic analysis revealed the occurrence of several independent events of gene loss and duplication across the different lineages of the genus Burkholderia, leading to notable differences in the number of paralogs between different genomes. A putative substrate [antibiotics (HAE1 proteins)/heavy-metal (HME proteins)] was also assigned to the majority of these proteins. No correlation was found between the ecological niche and the lifestyle of Burkholderia strains and the number/type of efflux pumps they possessed, while a relation can be found with genome size and taxonomy. Remarkably, we observed that only HAE1 proteins are mainly responsible for the different number of proteins observed in strains of the same species. Data concerning both the distribution and the phylogenetic analysis of the HAE1 and HME in the Burkholderia genus allowed depicting a likely evolutionary model accounting for the evolution and spreading of HME and HAE1 systems in the Burkholderia genus.ConclusionA complete knowledge of the presence and distribution of RND proteins in Burkholderia species was obtained and an evolutionary model was depicted. Data presented in this work may serve as a basis for future experimental tests, focused especially on HAE1 proteins, aimed at the identification of novel targets in antimicrobial therapy against Burkholderia species.
Highlights
The genus Burkholderia includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem
The analysis of each of the 16 plots and a comparison with the experimentally determined secondary structure of the E. coli AcrB and P. aeruginosa MexB, allowed to identify all the 12 transmembrane spanner (TMS) and the two large loops, that are characteristic of RND proteins
The analysis of conserved residues involved in different functions of Heavy Metal Efflux (HME) and Hydrophobe/Amphiphile Efflux-1 (HAE1) sequences allowed refining motifs previously identified on the basis of a smaller protein dataset
Summary
The genus Burkholderia includes a variety of species with opportunistic human pathogenic strains, whose increasing global resistance to antibiotics has become a public health problem. In this context a major role could be played by multidrug efflux pumps belonging to Resistance Nodulation Cell-Division (RND) family, which allow bacterial cells to extrude a wide range of different substrates, including antibiotics. Burkholderia spp. can be free-living in the rhizosphere as well as epiphytic and been demonstrated to be opportunistic pathogens in humans They are not considered pathogens for the normal human population, some are serious threats for specific patient groups. These species include B. gladioli, B. fungorum and all B. cepacia complex (BCC) bacteria [2]. The BCC is a group of genetically distinct but phenotypically similar bacteria that up to now comprises seventeen closely related bacterial species [1,3,4], and they are important opportunistic pathogens that infect the airways of cystic fibrosis (CF) patients [5]
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