Phylogenetic evidence for extensive horizontal gene transfer of type III secretion system genes among enterobacterial plant pathogens

Abstract

This study uses sequences from four genes, which are involved in the formation of the type III secretion apparatus, to determine the role of horizontal gene transfer in the evolution of virulence genes for the enterobacterial plant pathogens. Sequences of Erwinia, Brenneria, Pectobacterium, Dickeya and Pantoea were compared (a) with one another, (b) with sequences of enterobacterial animal pathogens, and (c) with sequences of plant pathogenic c and b proteobacteria, to evaluate probable paths of lateral exchange leading to the current distribution of virulence determinants among these micro-organisms. Phylogenies were reconstructed based on hrcC, hrcR, hrcJ and hrcV gene sequences using parsimony and maximum-likelihood algorithms. Virulence gene phylogenies were also compared with several housekeeping gene loci in order to evaluate patterns of lateral versus vertical acquisition. The resulting phylogenies suggest that multiple horizontal gene transfer events have occurred both within and among the enterobacterial plant pathogens and plant pathogenic c and b proteobacteria. hrcJ sequences are the most similar, exhibiting anywhere from 2 to 50 % variation at the nucleotide level, with the highest degree of variation present between plant and animal pathogen sequences. hrcV sequences are conserved among plant and animal pathogens at the N terminus. The C-terminal domain is conserved only among the enterobacterial plant pathogens, as are the hrcC and hrcR sequences. Additionally, hrcJ and hrcV sequence phylogenies suggest that at least some type III secretion system virulence genes from enterobacterial plant pathogens are related more closely to those of the genus Pseudomonas, a conclusion neither supported nor refuted by hrcC or hrcR.

Origins and Diversification of a Complex Signal Transduction System in Prokaryotes

“…In-depth sequenced-based analysis of the bacterial flagella revealed that flagellar components are vertically inherited (29). In our FlhA tree, the clade we assigned to be true FlhA proteins showed distinct taxonomic-based clades consistent with the previous findings, whereas the clade of 49 sequences predicted to be TTSS components showed sporadic groupings characteristic of horizontal transfer, which is common in TTSSs (79). Furthermore, 15 of the TTSS clade members are from Chlaymdia and Myxococcus species that have never been shown to have flagella, and 32 of the remaining TTSS clade members have representatives in the FlhA clade.…”

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

“…Therefore the conjugation systems we identify in genomes are expected to have neighboring integrases. Co-localization of MOBless T4SS with integrases is expected under a number of situations: (i) if the protein secretion system is in a mobile element itself, as is frequently the case for T3SS [65], [66]; (ii) if it represents an element undergoing genetic degradation is which the relaxase was inactivated but not the integrase nor the T4SS genes; (iii) or if the genes encoding the T4SS happen to be near an unrelated mobile element. Yet, since integration is strictly necessary for ICE, we did expect to find more integrases neighboring the T4SS of ICE than those of MOBless T4SS.…”

The awr Gene Family Encodes a Novel Class of Ralstonia solanacearum Type III Effectors Displaying Virulence and Avirulence Activities

“…1B), in which the origin of these effectors preceded the splitting of β-and γ-proteobacteria (Naum et al 2009;Tayeb et al 2008;Wu and Eisen 2008). From this origin, the gene family experienced several duplications or deletions in the γ-proteobacteria lineage.…”