Reanalysis of 5S rRNA sequence data for the Vibrionaceae with the clustan program suite

Vibrio chromosomes share common history

Background

While most gamma proteobacteria have a single circular chromosome, Vibrionales have two circular chromosomes. Horizontal gene transfer is common among Vibrios, and in light of this genetic mobility, it is an open question to what extent the two chromosomes themselves share a common history since their formation.

Results

Single copy genes from each chromosome (142 genes from chromosome I and 42 genes from chromosome II) were identified from 19 sequenced Vibrionales genomes and their phylogenetic comparison suggests consistent phylogenies for each chromosome. Additionally, study of the gene organization and phylogeny of the respective origins of replication confirmed the shared history.

Conclusions

Thus, while elements within the chromosomes may have experienced significant genetic mobility, the backbones share a common history. This allows conclusions based on multilocus sequence analysis (MLSA) for one chromosome to be applied equally to both chromosomes.

The evolutionary history of the structure of 5S ribosomal RNA

5S rRNA is the smallest nucleic acid component of the large ribosomal subunit, contributing to ribosomal assembly, stability, and function. Despite being a model for the study of RNA structure and RNA-protein interactions, the evolution of this universally conserved molecule remains unclear. Here, we explore the history of the three-domain structure of 5S rRNA using phylogenetic trees that are reconstructed directly from molecular structure. A total of 46 structural characters describing the geometry of 666 5S rRNAs were used to derive intrinsically rooted trees of molecules and molecular substructures. Trees of molecules revealed the tripartite nature of life. In these trees, superkingdom Archaea formed a paraphyletic basal group, while Bacteria and Eukarya were monophyletic and derived. Trees of molecular substructures supported an origin of the molecule in a segment that is homologous to helix I (alpha domain), its initial enhancement with helix III (beta domain), and the early formation of the three-domain structure typical of modern 5S rRNA in Archaea. The delayed formation of the branched structure in Bacteria and Eukarya lends further support to the archaeal rooting of the tree of life. Remarkably, the evolution of molecular interactions between 5S rRNA and associated ribosomal proteins inferred from a census of domain structure in hundreds of genomes established a tight relationship between the age of 5S rRNA helices and the age of ribosomal proteins. Results suggest 5S rRNA originated relatively quickly but quite late in evolution, at a time when primordial metabolic enzymes and translation machinery were already in place. The molecule therefore represents a late evolutionary addition to the ribosomal ensemble that occurred prior to the early diversification of Archaea.

The human pathogenic vibrios--a public health update with environmental perspectives

Pathogenic Vibrio species are naturally-occurring bacteria in freshwater and saline aquatic environments. Counts of free-living bacteria in water are generally less than required to induce disease. Increases in number of organisms towards an infective dose can occur as water temperatures rise seasonally followed by growth and concentration of bacteria on higher animals, such as chitinous plankton, or accumulation by shellfish and seafood. Pathogenic Vibrio species must elaborate a series of virulence factors to elicit disease in humans. Activities which predispose diarrhoeal and extraintestinal infections include ingestion of seafood and shellfish and occupational or recreational exposure to natural aquatic environments, especially those above 20 degrees C. Travel to areas endemic for diseases due to pathogenic Vibrio species may be associated with infections. Host risk factors strongly associated with infections are lack of gastric acid and liver disorders. Involvement of pathogenic Vibrio species in cases of diarrhoea should be suspected especially if infection is associated with ingestion of seafood or shellfish, raw or undercooked, in the previous 72 h. Vibrio species should be suspected in any acute infection associated with wounds sustained or exposed in the marine or estuarine environment. Laboratories serving coastal areas where infection due to pathogenic Vibrio species are most likely to occur should consider routine use of TCBS agar and other detection regimens for culture of Vibrio species from faeces, blood and samples from wound and ear infections.