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Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas.

ABSTRACT: Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in genome sequencing, comparative genome analysis provides a new approach to facilitate our understanding of these bacteria. In this study, our main focus is to investigate the evolution of gene content in phytoplasmas, mycoplasmas, and their common ancestor. By using a phylogenetic framework for comparative analysis of 12 complete genome sequences, we characterized the putative gains and losses of genes in these obligate parasites. Our results demonstrated that the degradation of metabolic capacities in these bacteria has occurred predominantly in the common ancestor of Mollicutes, prior to the evolutionary split of phytoplasmas and mycoplasmas. Furthermore, we identified a list of genes that are acquired by the common ancestor of phytoplasmas and are conserved across all strains with complete genome sequences available. These genes include several putative effectors for the interactions with hosts and may be good candidates for future functional characterization.

SUBMITTER: Chen LL

PROVIDER: S-EPMC3313985 | biostudies-literature | 2012

REPOSITORIES: biostudies-literature

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Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas.

Chen Ling-Ling LL Chung Wan-Chia WC Lin Chan-Pin CP Kuo Chih-Horng CH

PloS one 20120327 3

Phytoplasmas and mycoplasmas are two groups of important pathogens in the bacterial class Mollicutes. Because of their economical and clinical importance, these obligate pathogens have attracted much research attention. However, difficulties involved in the empirical study of these bacteria, particularly the fact that phytoplasmas have not yet been successfully cultivated outside of their hosts despite decades of attempts, have greatly hampered research progress. With the rapid advancements in g ...[more]

PMID: 22479625

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Project description:Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses.

Project description:BackgroundMycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.ResultsThe overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.ConclusionsThe comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host's immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.

Dataset Information

Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas.

Publications

Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas.

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