A robust species tree for the alphaproteobacteria.

Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
Journal of Bacteriology (Impact Factor: 2.69). 08/2007; 189(13):4578-86. DOI: 10.1128/JB.00269-07
Source: PubMed

ABSTRACT The branching order and coherence of the alphaproteobacterial orders have not been well established, and not all studies have agreed that mitochondria arose from within the Rickettsiales. A species tree for 72 alphaproteobacteria was produced from a concatenation of alignments for 104 well-behaved protein families. Coherence was upheld for four of the five orders with current standing that were represented here by more than one species. However, the family Hyphomonadaceae was split from the other Rhodobacterales, forming an expanded group with Caulobacterales that also included Parvularcula. The three earliest-branching alphaproteobacterial orders were the Rickettsiales, followed by the Rhodospirillales and then the Sphingomonadales. The principal uncertainty is whether the expanded Caulobacterales group is more closely associated with the Rhodobacterales or the Rhizobiales. The mitochondrial branch was placed within the Rickettsiales as a sister to the combined Anaplasmataceae and Rickettsiaceae, all subtended by the Pelagibacter branch. Pelagibacter genes will serve as useful additions to the bacterial outgroup in future evolutionary studies of mitochondrial genes, including those that have transferred to the eukaryotic nucleus.

Download full-text


Available from: Allan W Dickerman, Jul 05, 2015
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Mitochondria are eukaryotic organelles which contain the own genetic material and evolved from free-living eubacteria, namely hydrogen-producing Alphaproteobacteria. Since 1965, biologists provided, by research at molecular level, evidence for the prokaryotic origins of mitochondria. However, determining the precise origins of mitochondria is challenging due to inherent difficulties in phylogenetically reconstructing ancient evolutionary events. The use of new tools to evidence the prokaryotic origin of mitochondria could be useful to gain an insight into the bacterial endosymbiotic event that resulted in the permanent acquisition of bacteria, from the ancestral cell, that through time were transformed into mitochondria. Electron microscopy has shown that both proteobacterial and yeast cells during their growth in the presence of increasing amount of tellurite resulted in dose-dependent blackening of the culture due to elemental tellurium (Te0) that formed large deposits either along the proteobacterial membrane or along the yeast cell wall and mitochondria. Since the mitochondrial inner membrane composition is similar to that of proteobacterial membrane, in the present work we evidenced the black tellurium deposits on both, cell wall and mitochondria of ρ+ and respiratory deficient ρ- mutants of yeast. A possible role of tellurite in studying the evolutionary origins of mitochondria will be discussed
    Gene 01/2015; 559(2). DOI:10.1016/j.gene.2015.01.060 · 2.08 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Amoebae serve as hosts for various intracellular bacteria, including human pathogens. These microbes are able to overcome amoebal defense mechanisms and successfully establish a niche for replication, which is usually the cytoplasm. Here, we report on the discovery of a bacterial symbiont that is located inside the nucleus of its Hartmannella sp. host. This symbiont, tentatively named 'Candidatus Nucleicultrix amoebiphila', is only moderately related to known bacteria (∼90% 16S and 23S rRNA sequence similarity) and member of a novel clade of protist symbionts affiliated with the Rickettsiales and Rhodospirillales. Screening of 16S rRNA amplicon data sets revealed a broad distribution of these bacteria in freshwater and soil habitats. 'Candidatus Nucleicultrix amoebiphila' traffics within 6 h post infection to the host nucleus. Maximum infection levels are reached after 96-120 h, at which time point the nucleus is pronouncedly enlarged and filled with bacteria. Transmission of the symbionts occurs vertically upon host cell division but may also occur horizontally through host cell lysis. Although we observed no impact on the fitness of the original Hartmannella sp. host, the bacteria are rather lytic for Acanthamoeba castellanii. Intranuclear symbiosis is an exceptional phenomenon, and amoebae represent an ideal model system to further investigate evolution and underlying molecular mechanisms of these unique microbial associations.The ISME Journal advance online publication, 6 February 2014; doi:10.1038/ismej.2014.5.
    The ISME Journal 02/2014; DOI:10.1038/ismej.2014.5 · 9.27 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Phylogenomic analyses are subject to bias from compositional convergence and noise from horizontal gene transfer (HGT). Compositional convergence is a likely cause of controversy regarding phylogeny of the SAR11 group of Alphaproteobacteria that have extremely streamlined, A+T-biased genomes. While careful modeling can reduce artifacts caused by convergence, the most consistent and robust phylogenetic signal in genomes may lie distributed among encoded functional features that govern macromolecular interactions. Here we develop a novel phyloclassification method based on signatures derived from bioinformatically defined tRNA Class-Informative Features (CIFs). tRNA CIFs are enriched for features that underlie tRNA-protein interactions. Using a simple tRNA-CIF-based phyloclassifier, we obtained results consistent with those of bias-corrected whole proteome phylogenomic studies, rejecting monophyly of SAR11 and affiliating most strains with Rhizobiales with strong statistical support. Yet SAR11 and Rickettsiales tRNA genes share distinct patterns of A+T-richness, as expected from their elevated genomic A+T compositions. Using conventional supermatrix methods on total tRNA sequence data, we could recover the artifactual result of a monophyletic SAR11 grouping with Rickettsiales. Thus tRNA CIF-based phyloclassification is more robust to base content convergence than supermatrix phylogenomics on whole tRNA sequences. Also, given the notoriously promiscuous HGT of aminoacyl-tRNA synthetases, tRNA CIF-based phyloclassification may be relatively robust to HGT of network components. We describe how unique features of tRNA-protein interaction networks facilitate the mining of traits governing macromolecular interactions from genomic data, and discuss why interaction-governing traits may be especially useful to solve difficult problems in microbial classification and phylogeny.