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Bern, Marshall; Goldberg, David

doi:10.1186/1471-2148-5-34

Cited by 27 publications

(10 citation statements)

References 55 publications

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“…3). The resulting topology is in good agreement with rRNA trees [27], recently published concatenated-protein phylogenies [28,29], as well as supertree phylogenies [30]. In particular, we do recover the clade named "Terrabacteria" by Battistuzzi and co-workers, as well as the clade named Gracilicutes by Cavalier-Smith [7], separated with a high bootstrap support (BS 94%).…”

Section: Resultssupporting

confidence: 84%

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

2008

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BackgroundDespite a large agreement between ribosomal RNA and concatenated protein phylogenies, the phylogenetic tree of the bacterial domain remains uncertain in its deepest nodes. For instance, the position of the hyperthermophilic Aquificales is debated, as their commonly observed position close to Thermotogales may proceed from horizontal gene transfers, long branch attraction or compositional biases, and may not represent vertical descent. Indeed, another view, based on the analysis of rare genomic changes, places Aquificales close to epsilon-Proteobacteria.ResultsTo get a whole genome view of Aquifex relationships, all trees containing sequences from Aquifex in the HOGENOM database were surveyed. This study revealed that Aquifex is most often found as a neighbour to Thermotogales. Moreover, informational genes, which appeared to be less often transferred to the Aquifex lineage than non-informational genes, most often placed Aquificales close to Thermotogales. To ensure these results did not come from long branch attraction or compositional artefacts, a subset of carefully chosen proteins from a wide range of bacterial species was selected for further scrutiny. Among these genes, two phylogenetic hypotheses were found to be significantly more likely than the others: the most likely hypothesis placed Aquificales as a neighbour to Thermotogales, and the second one with epsilon-Proteobacteria. We characterized the genes that supported each of these two hypotheses, and found that differences in rates of evolution or in amino-acid compositions could not explain the presence of two incongruent phylogenetic signals in the alignment. Instead, evidence for a large Horizontal Gene Transfer between Aquificales and epsilon-Proteobacteria was found.ConclusionMethods based on concatenated informational proteins and methods based on character cladistics led to different conclusions regarding the position of Aquificales because this lineage has undergone many horizontal gene transfers. However, if a tree of vertical descent can be reconstructed for Bacteria, our results suggest Aquificales should be placed close to Thermotogales.

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Section: Resultssupporting

confidence: 84%

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

2008

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“…Among this set of marker genes, the COG0012 gene (a ribosome-associated GTPase) has a number of beneficial traits. In earlier studies, this COG was shown to be useful for inferring phylogenetic relationships with high fidelity, yielding results that are congruent with ribosomal RNA analyses (Harris, 2003; Bern and Goldberg, 2005; Mende et al, 2013). In addition to the phylogenetic resolution COG0012 provides, its features suggest it as a useful marker for defining relationships among closely related microbial taxa.…”

Section: Methodsmentioning

confidence: 58%

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre

2019

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Marine microbial communities are responsible for many important ecosystem processes in the oceans. Their variability across time and depths is well recognized, but mostly at a coarse-grained taxonomic resolution. To gain a deeper perspective on ecological patterns of bacterioplankton diversity in the North Pacific Subtropical Gyre, we characterized bacterioplankton communities throughout the water column at a fine-grained taxonomic level with a focus on temporally persistent (core) populations. Considerable intra-clade microdiversity was evident in virtually every microbial clade examined. While some of the most abundant populations comprised only a small fraction of the intra-clade microdiversity, they formed a temporally persistent core within a more diverse array of less abundant ephemeral populations. The depth-stratified population structure within many phylogenetically disparate clades suggested that ecotypic variation was the rule among most planktonic bacterial and archaeal lineages. Our results suggested that the abundant, persistent core populations comprised the bulk of the biomass within any given clade. As such, we postulate that these core populations are largely responsible for microbially driven ecosystem processes, and so represent ideal targets for elucidating key microbial processes in the open-ocean water column.

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“…However, the novelty of this contribution is that by using the iterative bio-informatics approach, we can show that the WXG100 protein superfamily can be divided into three subfamilies: CFP-10-, ESAT-6- and sag EsxA-like. In addition, the phylogeny analysis of WXG proteins indicates that the Actinobacteria might be evolutionarily closer to the bacterial phylum Firmicutes than previously thought [27]. Subsequent analyses of the genetic organisation of WXG100 genes show that CFP-10- and ESAT-6-like genes are always encoded together on a bi -cistronic operon in contrast to the mono-cistronic s ag EsxA-like genes.…”

Section: Discussionmentioning

confidence: 91%

WXG100 Protein Superfamily Consists of Three Subfamilies and Exhibits an α-Helical C-Terminal Conserved Residue Pattern

Paar¹,

Panjikar

Holton³

et al. 2014

PLoS ONE

103

106

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Members of the WXG100 protein superfamily form homo- or heterodimeric complexes. The most studied proteins among them are the secreted T-cell antigens CFP-10 (10 kDa culture filtrate protein, EsxB) and ESAT-6 (6 kDa early secreted antigen target, EsxA) from Mycobacterium tuberculosis. They are encoded on an operon within a gene cluster, named as ESX-1, that encodes for the Type VII secretion system (T7SS). WXG100 proteins are secreted in a full-length form and it is known that they adopt a four-helix bundle structure. In the current work we discuss the evolutionary relationship between the homo- and heterodimeric WXG100 proteins, the basis of the oligomeric state and the key structural features of the conserved sequence pattern of WXG100 proteins. We performed an iterative bioinformatics analysis of the WXG100 protein superfamily and correlated this with the atomic structures of the representative WXG100 proteins. We find, firstly, that the WXG100 protein superfamily consists of three subfamilies: CFP-10-, ESAT-6- and sagEsxA-like proteins (EsxA proteins similar to that of Streptococcus agalactiae). Secondly, that the heterodimeric complexes probably evolved from a homodimeric precursor. Thirdly, that the genes of hetero-dimeric WXG100 proteins are always encoded in bi-cistronic operons and finally, by combining the sequence alignments with the X-ray data we identify a conserved C-terminal sequence pattern. The side chains of these conserved residues decorate the same side of the C-terminal α-helix and therefore form a distinct surface. Our results lead to a putatively extended T7SS secretion signal which combines two reported T7SS recognition characteristics: Firstly that the T7SS secretion signal is localized at the C-terminus of T7SS substrates and secondly that the conserved residues YxxxD/E are essential for T7SS activity. Furthermore, we propose that the specific α-helical surface formed by the conserved sequence pattern including YxxxD/E motif is a key component of T7SS-substrate recognition.

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Untitled

Cited by 27 publications

References 55 publications

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Accounting for horizontal gene transfers explains conflicting hypotheses regarding the position of aquificales in the phylogeny of Bacteria

Persistent Core Populations Shape the Microbiome Throughout the Water Column in the North Pacific Subtropical Gyre

WXG100 Protein Superfamily Consists of Three Subfamilies and Exhibits an α-Helical C-Terminal Conserved Residue Pattern

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