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: 2.81). 08/2007; 189(13):4578-86. DOI: 10.1128/JB.00269-07
Source: PubMed


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.

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    • "The best candidate source for this bacterium is also still α-proteobacteria (Gray 2012; Müller et al. 2012; Esposti 2014). This is primarily because most of the few remaining genes in mitochondrial genomes (mtDNAs) show α-proteobacterial affinity (Andersson et al. 2003; Esser et al. 2004; Fitzpatrick et al. 2006; Williams et al. 2007; Rodríguez-Ezpeleta and Embley 2012), as do 10-20% of the nuclear genes that encode 95-99% of the mitochondrial proteome (Szklarczyk and Huynen 2010; Thiergart et al. 2012; Gray 2015). Thus α-proteobacterial-like nuclear genes encoding mitochondrial proteins are presumed to have originated by transfer of genetic material from the mitochondrion to the nucleus (endosymbiotic gene transfer or EGT) (Timmis et al. 2004). "
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    ABSTRACT: The most gene-rich and bacterial-like mitochondrial genomes (mtDNAs) known are those of Jakobida (Excavata). Of these, the most extreme example to date is the Andalucia godoyi mtDNA, including a cox15 gene encoding the respiratory enzyme heme A synthase (HAS), which is nuclear-encoded in nearly all other mitochondriate eukaryotes. Thus cox15 in eukaryotes appears to be a classic example of mitochondrion-to-nucleus (endosymbiotic) gene transfer, with A. godoyi uniquely retaining the ancestral state. However, our analyses reveal two highly distinct HAS types (encoded by cox15-1 and cox15-2 genes) and identify A. godoyi mitochondrial cox15-encoded HAS as type-1 and all other eukaryotic cox15-encoded HAS as type-2. Molecular phylogeny places the two HAS types in widely separated clades with eukaryotic type-2 HAS clustering with the bulk of α-proteobacteria (>670 sequences), while A. godoyi type-1 HAS clusters with an eclectic set of bacteria and archaea including two α-proteobacteria missing from the type-2 clade. This wide phylogenetic separation of the two HAS types is reinforced by unique features of their predicted protein structures. Meanwhile, RNA-sequencing and genomic analyses fail to detect either cox15 type in the nuclear genome of any jakobid including A. godoyi. This suggests that not only is cox15-1 a relatively recent acquisition unique to the Andalucia lineage, but the jakobid last common ancestor probably lacked both cox15 types. These results indicate that uptake of foreign genes by mtDNA is more taxonomically widespread than previously thought. They also caution against the assumption that all α-proteobacterial-like features of eukaryotes are ancient remnants of endosymbiosis.
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    • "Odyssella thessalonicensis, (Georgiades et al., 2011), Lyticum, (Boscaro et al., 2013) and Trichorickettsia and Gigarickettsia (Vannini et al., 2014) are examples that contradict the previous assumption that flagella were lost in all Rickettsiales and fortifies the suggestion that flagella were present in the last common Rickettsiales ancestor. The Rickettsiales have traditionally been put forward as candidates for the closest relatives of mitochondria (Fitzpatrick et al., 2006; Williams et al., 2007). However, there is still no consensus about exact phylogenetic placement of mitochondria . "
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    ABSTRACT: The bacterial family Rickettsiaceae includes a group of well-known etiological agents of many human and vertebrate diseases, including epidemic typhus-causing pathogen Rickettsia prowazekii. Owing to their medical relevance, rickettsiae have attracted a great deal of attention and their host-pathogen interactions have been thoroughly investigated. All known members display obligate intracellular lifestyles, and the best-studied genera, Rickettsia and Orientia, include species that are hosted by terrestrial arthropods. Their obligate intracellular lifestyle and host adaptation is reflected in the small size of their genomes, a general feature shared with all other families of the Rickettsiales. Yet, despite that the Rickettsiaceae and other Rickettsiales families have been extensively studied for decades, many details of the origin and evolution of their obligate host-association remain elusive. Here we report the discovery and single-cell sequencing of 'Candidatus Arcanobacter lacustris', a rare environmental alphaproteobacterium that was sampled from Damariscotta Lake that represents a deeply rooting sister lineage of the Rickettsiaceae. Intriguingly, phylogenomic and comparative analysis of the partial 'Candidatus Arcanobacter lacustris' genome revealed the presence chemotaxis genes and vertically inherited flagellar genes, a novelty in sequenced Rickettsiaceae, as well as several host-associated features. This finding suggests that the ancestor of the Rickettsiaceae might have had a facultative intracellular lifestyle. Our study underlines the efficacy of single-cell genomics for studying microbial diversity and evolution in general, and for rare microbial cells in particular.
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    • "In a landmark study, Dumler et al. (2001) meticulously placed the majority of the species in these five genera into Neorickettsia, Wolbachia, Anaplasma, and Ehrlichia, with substantial revision of the latter two genera. Robust phylogeny estimations have supported the monophyly of the contemporary Anaplasmataceae, and its sister relationship with the Rickettsiaceae within Rickettsiales (Williams et al. 2007, Gillespie et al. 2012b, Driscoll et al. 2013). Neorickettsia spp. "
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