Dataset Information

Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp.

ABSTRACT: Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were found in 15 Pantoea genomes. These ars clusters were found to be acquired by horizontal gene transfer (HGT) from sources related to Franconibacter helveticus, Serratia marcescens, and Citrobacter freundii. During the history of evolution, the ars clusters were acquired more than once in some species, and were lost in some strains, producing strains without As resistance capability. This study revealed the organization, distribution and the complex evolutionary history of As resistance genes in Pantoea spp.. The insights gained in this study improved our understanding on the As resistance strategy of Pantoea spp. and its roles in the biogeochemical cycling of As.

SUBMITTER: Wang L

PROVIDER: S-EPMC5360009 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp.

Wang Liying L Wang Jin J Jing Chuanyong C

Frontiers in microbiology 20170321

Numerous genes are involved in various strategies to resist toxic arsenic (As). However, the As resistance strategy in genus Pantoea is poorly understood. In this study, a comparative genome analysis of 23 Pantoea genomes was conducted. Two vertical genetic arsC-like genes without any contribution to As resistance were found to exist in the 23 Pantoea strains. Besides the two arsC-like genes, As resistance gene clusters arsRBC or arsRBCH were foun ...[more]

PMID: 28377759

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Project description:Members of the genus Acidithiobacillus, which can adapt to extremely high concentrations of heavy metals, are universally found at acid mine drainage (AMD) sites. Here, we performed a comparative genomic analysis of 37 strains within the genus Acidithiobacillus to answer the untouched questions as to the mechanisms and the evolutionary history of metal resistance genes in Acidithiobacillus spp. The results showed that the evolutionary history of metal resistance genes in Acidithiobacillus spp. involved a combination of gene gains and losses, horizontal gene transfer (HGT), and gene duplication. Phylogenetic analyses revealed that metal resistance genes in Acidithiobacillus spp. were acquired by early HGT events from species that shared habitats with Acidithiobacillus spp., such as Acidihalobacter, Thiobacillus, Acidiferrobacter, and Thiomonas species. Multicopper oxidase genes involved in copper detoxification were lost in iron-oxidizing Acidithiobacillus ferridurans, Acidithiobacillus ferrivorans, and Acidithiobacillus ferrooxidans and were replaced by rusticyanin genes during evolution. In addition, widespread purifying selection and the predicted high expression levels emphasized the indispensable roles of metal resistance genes in the ability of Acidithiobacillus spp. to adapt to harsh environments. Altogether, the results suggested that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. This study sheds light on the distribution, organization, functionality, and complex evolutionary history of metal resistance genes in Acidithiobacillus spp.IMPORTANCE Horizontal gene transfer (HGT), natural selection, and gene duplication are three main engines that drive the adaptive evolution of microbial genomes. Previous studies indicated that HGT was a main adaptive mechanism in acidophiles to cope with heavy-metal-rich environments. However, evidences of HGT in Acidithiobacillus species in response to challenging metal-rich environments and the mechanisms addressing how metal resistance genes originated and evolved in Acidithiobacillus are still lacking. The findings of this study revealed a fascinating phenomenon of putative cross-phylum HGT, suggesting that Acidithiobacillus spp. recruited and consolidated additional novel functionalities during the adaption to challenging environments via HGT, gene duplication, and purifying selection. Altogether, the insights gained in this study have improved our understanding of the metal resistance strategies of Acidithiobacillus spp.

Project description:BackgroundThe cattle UL16-binding protein 1 (ULBP1) and ULBP2 genes encode members of the MHC Class I superfamily that have homology to the human ULBP genes. Human ULBP1 and ULBP2 interact with the NKG2D receptor to activate effector cells in the immune system. The human cytomegalovirus UL16 protein is known to disrupt the ULBP-NKG2D interaction, thereby subverting natural killer cell-mediated responses. Previous Southern blotting experiments identified evidence of increased ULBP copy number within the genomes of ruminant artiodactyls. On the basis of these observations we hypothesized that the cattle ULBPs evolved by duplication and sequence divergence to produce a sufficient number and diversity of ULBP molecules to deliver an immune activation signal in the presence of immunogenic peptides. Given the importance of the ULBPs in antiviral immunity in other species, our goal was to determine the copy number and genomic organization of the ULBP genes in the cattle genome.ResultsSequencing of cattle bacterial artificial chromosome genomic inserts resulted in the identification of 30 cattle ULBP loci existing in two gene clusters. Evidence of extensive segmental duplication and approximately 14 Kbp of novel repetitive sequences were identified within the major cluster. Ten ULBPs are predicted to be expressed at the cell surface. Substitution analysis revealed 11 outwardly directed residues in the predicted extracellular domains that show evidence of positive Darwinian selection. These positively selected residues have only one residue that overlaps with those proposed to interact with NKG2D, thus suggesting the interaction with molecules other than NKG2D.ConclusionThe ULBP loci in the cattle genome apparently arose by gene duplication and subsequent sequence divergence. Substitution analysis of the ULBP proteins provided convincing evidence for positive selection on extracellular residues that may interact with peptide ligands. These results support our hypothesis that the cattle ULBPs evolved under adaptive diversifying selection to avoid interaction with a UL16-like molecule whilst preserving the NKG2D binding site. The large number of ULBPs in cattle, their extensive diversification, and the high prevalence of bovine herpesvirus infections make this gene family a compelling target for studies of antiviral immunity.

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Comparative Genomic Analysis Reveals Organization, Function and Evolution of ars Genes in Pantoea spp.

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Comparative Genomic Analysis Reveals Organization, Function and Evolution of <i>ars</i> Genes in <i>Pantoea</i> spp.

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