Exploring the HME and HAE1 efflux systems in the genus BurkholderiaReport as inadecuate




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BMC Evolutionary Biology

, 10:164

First Online: 03 June 2010Received: 18 September 2009Accepted: 03 June 2010

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 functions 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.

AbbreviationsAPPEAryl Polyene Pigment Exporter

BCCBurkholderia cepacia complex

CFCystic fibrosis

EEnviromental

ESTEukaryotic putative Sterol transporter

HHost

HAE-1Hydrophobe Amphiphile Efflux-1

HAE-2Hydrophobe-Amphiphile Efflux-2

HAE-3Hydrophobe-Amphiphile Efflux-3

HGTHorizontal Gene Transfer

HMEHeavy-Metal Efflux

MbpMega Base Pair

MFPMembrane Fusion Protein

NCNot classified

NFEputative Nodulation Factor Exporter

NJNeighbor-Joining

OMPOuter-Membrane Protein

PPathogen

RNDResistance-Nodulation-Cell Division

SecDFSecretion System DF

TCDBTransport Classification Database

TMSTransMembrane Spanner.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2148-10-164 contains supplementary material, which is available to authorized users.

Elena Perrin, Marco Fondi contributed equally to this work.

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Author: Elena Perrin - Marco Fondi - Maria Cristiana Papaleo - Isabel Maida - Silvia Buroni - Maria Rosalia Pasca - Giovanna Ricc

Source: https://link.springer.com/article/10.1186/1471-2148-10-164



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