Clustal Omega

Sievers, Fabian; Higgins, Desmond G.

doi:10.1002/0471250953.bi0313s48

Cited by 593 publications

(474 citation statements)

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“…Subsequently, we generated local protein and nucleic acid Blast databases of all of the coding sequences of the pangenome, from which we extracted, in FASTA format, the nucleotide and amino acid sequences of these genes by use of the blastdbcmd tool of BLASTϩϩ (23). Then we aligned the amino acid sequences and generated protein sequence identity matrices with Clustal Omega (24). Subsequently, protein alignments were converted into codon-based nucleotide alignments with PAL2NAL (25).…”

Section: Methodsmentioning

confidence: 99%

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

Perez

Juniper

2016

Appl Environ Microbiol

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The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that "Ca. Endoriftia persephone" symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity. IMPORTANCERemarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, "Candidatus Endoriftia persephone." Understanding the structure, dynamism, and interconnectivity of "Ca. Endoriftia persephone" populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge. We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the "Ca. Endoriftia persephone" pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of "Ca. Endoriftia persephone" assemblies in the context of population genetics and molecular evolution.A defining characteristic of hydrothermal vent ecosystems is the diversity and ubiquity of mutualistic partnerships between metazoa (multicellular organisms) and chemolithoautotrophic bacteria. Among these associations, one of the most remarkable is the well-studied model symbiosis between the giant tubeworm Riftia pachyptila and its unique sulfide-oxidizing gammaproteobacterial partner, "Candidatus Endoriftia persephone" (1). These intracellular symbionts are hosted within the specialized cells (bacteriocytes) of an organ known as the trophosome, which occupies most of the space in the coelomic cavity of the animal's trunk. In this mutualistic association, the worm supplies the bacteria with the inorganic compounds necessary for coupling sulfide oxidatio...

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Section: Methodsmentioning

confidence: 99%

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

Perez

Juniper

2016

Appl Environ Microbiol

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“…Glycosyltransferases showing (i) several TMDs predicted by TMHMM2 (31) with a large cytoplasmic loop bearing DXD and R/QXXRW-like motifs (identified by alignment with the galactan synthase MSC_0108 with Clustal Omega [32]) and (ii) homology with the cellulose synthase of Rhodobacter sphaeroides cellulose synthase subunit a (Uniprot accession number Q3J125) as shown using Phyre (33) were classified as synthases. Transmembrane proteins (see Fig.…”

Section: Methodsmentioning

confidence: 99%

Mycoplasma agalactiae Secretion of β-(1→6)-Glucan, a Rare Polysaccharide in Prokaryotes, Is Governed by High-Frequency Phase Variation

Gaurivaud

Baranowski

Pau-Roblot

et al. 2016

Appl Environ Microbiol

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Mycoplasmas are minimal, wall-less bacteria but have retained the ability to secrete complex carbohydrate polymers that constitute a glycocalyx. In members of the Mycoplasma mycoides cluster, which are important ruminant pathogens, the glycocalyx includes both cell-attached and cell-free polysaccharides. This report explores the potential secretion of polysaccharides by M. agalactiae, another ruminant pathogen that belongs to a distant phylogenetic group. Comparative genomic analyses showed that M. agalactiae possesses all the genes required for polysaccharide secretion. Notably, a putative synthase gene (gsmA) was identified, by in silico reconstruction of the biosynthetic pathway, that could be involved in both polymerization and export of the carbohydrate polymers. M. agalactiae polysaccharides were then purified in vitro and found to be mainly cell attached, with a linear ␤-(1¡6)-glucopyranose structure [␤-(1¡6)-glucan]. Secretion of ␤-(1¡6)-glucan was further shown to rely on the presence of a functional gsmA gene, whose expression is subjected to high-frequency phase variation. This event is governed by the spontaneous intraclonal variation in length of a poly(G) tract located in the gsmA coding sequence and was shown to occur in most of the M. agalactiae clinical isolates tested in this study. M. agalactiae susceptibility to serum-killing activity appeared to be dictated by ON/OFF switching of ␤-(1¡6)-glucan secretion, suggesting a role of this phenomenon in survival of the pathogen when it invades the host bloodstream. Finally, ␤-(1¡6)-glucan secretion was not restricted to M. agalactiae but was detected also in M. mycoides subsp. capri PG3 T , another pathogen of small ruminants. IMPORTANCEMany if not all bacteria are able to secrete polysaccharides, either attached to the cell surface or exported unbound into the extracellular environment. Both types of polysaccharides can play a role in bacterium-host interactions. Mycoplasmas are no exception despite their poor overall metabolic capacity. We showed here that M. agalactiae secretes a capsular ␤-(1¡6)-glucopyranose thanks to a specific glycosyltransferase with synthase activity. This secretion is governed by high-frequency ON/OFF phase variation that might be crucial in mycoplasma host dissemination, as cell-attached ␤-(1¡6)-glucopyranose increases serum-killing susceptibility. Our results provide functional genetic data about mycoplasmal glycosyltransferases with dual functions, i.e., assembly and export of the sugar polymers across the cell membrane. Furthermore, we demonstrated that nonprotein epitopes can be subjected to surface antigenic variation in mycoplasmas. Finally, the present report contributes to unravel the role of secreted polysaccharides in the virulence and pathogenicity of these peculiar bacteria.

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“…The structures for the major human SULF1 and SULF2 trancripts were obtained using the AceView website (http://www.ncbi.nlm.nih.gov/ieb/research/acembly/) [26]. Alignments of SULF sequences with human SULF1 and SULF2 protein sequences were assembled using the Clustal Omega multiple sequence alignment program [31]. Predicted micro-RNA binding sites (miR) and CpG islands [32] were examined using the UCSC Genome Browser [27].…”

Section: Introductionmentioning

confidence: 99%

Comparative and Evolutionary Studies of Vertebrate Extracellular Sulfatase Genes and Proteins: SULF1 and SULF2

Holmes¹

2017

J Proteomics Bioinform

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Clustal Omega

Cited by 593 publications

References 22 publications

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

Insights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers

Mycoplasma agalactiae Secretion of β-(1→6)-Glucan, a Rare Polysaccharide in Prokaryotes, Is Governed by High-Frequency Phase Variation

Comparative and Evolutionary Studies of Vertebrate Extracellular Sulfatase Genes and Proteins: SULF1 and SULF2

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