Ancient origin of reggie (flotillin), reggie-like, and other lipid-raft proteins : convergent evolution of the SPFH domain

Reggies (flotillins) are detergent-resistant microdomains involved in the scaffolding of large heteromeric complexes that signal across the plasma membrane. Based on the presence of an evolutionarily widespread motif, reggies/flotillins have been included within the SPFH (stomatin-prohibitin-flotillin-HflC/K) protein superfamily. To better understand the origin and evolution of reggie/flotillin structure and function, we searched databases for reggie/flotillin and SPFH-like proteins in organisms at the base and beyond the animal kingdom, and used the resulting dataset to compare their structural and functional domains. Our analysis shows that the SPFH grouping has little phylogenetic support, probably due to convergent evolution of its members. We also find that reggie/flotillin homologues are highly conserved among metazoans but are absent in plants, fungi and bacteria, where only proteins with "reggie-like" domains can be found. However, despite their low sequence similarities, reggie/flotillin and "reggie-like" domains appear to subserve related functions, suggesting that their basic biological role was acquired independently during evolution

An evolutionary basis for scrapie disease : identification of a fish prion mRNA

Infectious prion proteins cause neurodegenerative disease in mammals owing to the acquisition of an aberrant conformation. We cloned a Fugu rubripes gene that encodes a structurally conserved prion protein, and found rapid rates of molecular divergence among prions from different vertebrate classes, along with molecular stasis within each class. We propose that a directional trend in the evolution of prion sequence motifs associated with pathogenesis and infectivity could account for the origin of scrapie in mammals

Restricted Expression of Reggie Genes and Proteins during Early Zebrafish Development

Reggies are plasma membrane-associated proteins and characteristic markers of lipidraft microdomains. They are highly conserved from flies to humans and have been implicated in axon regeneration and cell process and contact formation, possibly providing functional platforms for cell-signaling in neurons and other cell types. We analyzed reggie mRNA and protein expression patterns during early zebrafish development. All three zebrafish genes, re-1a, -2a, and -2b, span a considerably diverse set of expression patterns, and their proteins are induced maternally, showing ubiquitous expression at early stages. Although re-2a mRNA can be observed in differentiating neurons in the brain, spinal cord, and neurogenic placodes, re-2b is transcribed mainly in head mesoderm, in neural crest derivates, and along somite boundaries. re-1a mRNA is present at high levels in expression domains that overlap with the combined expression pattern of both re-2 genes except at the somites, where it complements the pattern of re-2b. Immunostaining on embryos reveals reggie protein localization at the cell membrane, at cell cell contacts, and along all early axon tracts. The early phase of reggie expression suggests a basic and ubiquitous function during the first stages of embryogenesis and into the gastrula period. Upon segmentation, a second phase of expression shows distinctly localized expression patterns, indicating tissue-specific roles and an involvement of re-1a/re-2a in neural development

Evolutionary Analysis and Expression of Teleost Thy-1

Thy-1 is a developmentally regulated, immunoglobulin superfamily member (IgSF), glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein expressed most strongly in neurons and lymphocytes. Thy-1 is expressed in all vertebrates and has been implicated in a variety of processes, including axon regeneration and transmembrane signaling, but its specific function remains elusive. A Thy-1-like molecule in teleost fish was recently identified, with evidence for its role in lipid-raft based signal transduction linked to optic nerve regeneration. For a better characterization of Thy-1, the evolutionary relationships between novel fish homologues and other vertebrate Thy-1s were analyzed. Although the sequence similarity between fish and mammals is very low, there appeared conservation of gene structure and disrupted but recognizable synteny. In addition, the detailed expression analysis of teleost Thy-1 showed nervous system Thy-1 mainly in sensory systems. Strong Thy-1 expression was detected in the youngest retinal ganglion cells and in some neurons in deeper retinal layers, probably amacrine cells. From the olfactory bulbs, Thy-1-positive cells extended axons into the telencephalon. The vagal lobe stained intensively as well as facial and glossopharyngeal lobes and nerves. Outside the CNS, skin cells, blood vessels, kidney macrophages, swim bladder, spleen, gut-associated nerve fibers and the palatal organ were labeled

Evolutionary Analysis and Expression of Teleost Thy-1

ABSTRACT Thy-1 is a developmentally regulated, immunoglobulin superfamily member (IgSF), glycosylphosphatidylinositol (GPI)-anchored cell surface glycoprotein expressed most strongly in neurons and lymphocytes. Thy-1 is expressed in all vertebrates and has been implicated in a variety of processes, including axon regeneration and transmembrane signaling, but its specific function remains elusive. A Thy-1-like molecule in teleost fish was recently identified, with evidence for its role in lipid-raft based signal transduction linked to optic nerve regeneration. For a better characterization of Thy-1, the evolutionary relationships between novel fish homologues and other vertebrate Thy-1s were analyzed. Although the sequence similarity between fish and mammals is very low, there appeared conservation of gene structure and disrupted but recognizable synteny. In addition, the detailed expression analysis of teleost Thy-1 showed nervous system Thy-1 mainly in sensory systems. Strong Thy-1 expression was detected in the youngest retinal ganglion cells and in some neurons in deeper retinal layers, probably amacrine cells. From the olfactory bulbs, Thy-1-positive cells extended axons into the telencephalon. The vagal lobe stained intensively as well as facial and glossopharyngeal lobes and nerves. Outside the CNS, skin cells, blood vessels, kidney macrophages, swim bladder, spleen, gut-associated nerve fibers and the palatal organ were labeled. 19

Disparate evolution of prion protein domains and the distinct origin of Doppel- and prion-related loci revealed by fish-to-mammal comparisons

Our current understanding of prion biology and disease is largely based on studies performed on mammals, yet basic questions about the physiological function of prion proteins (PrPs) and the molecular nature of prion disorders remain elusive. To facilitate the establishment of non-mammalian models for prion research, we characterized the sequence, structural, and genomic homology between fish and other vertebrate PrPs, and analyzed the distinct molecular mechanisms that shaped the evolution of vertebrate PrP domains

An application of competitive reporter monitored amplification (CMA) for rapid detection of single nucleotide polymorphisms (SNPs)

<div><p>Single nucleotide polymorphisms (SNPs) are essential parameters in molecular diagnostics and can be used for the early detection and clinical prognosis in various diseases. Available methods for SNP detection are still labor-intensive and require a complex laboratory infrastructure, which are not suitable for the usage in resource-limited settings. Thus, there is an urgent need for a simple, reliable and rapid approach. In this paper we modified the previously developed competitive reporter monitored amplification (CMA) technique for the detection of resistance mediating SNPs in <i>Mycobacterium tuberculosis</i> complex (MTBC) strains. As a proof-of-principle for the application of the CMA-based SNP assay in routine molecular tuberculosis diagnostic, we show that the assay recognizes resistance mediating SNPs for rifampicin, isoniazid and ethambutol from either isolated DNA or heat inactivated <i>M</i>. <i>tuberculosis</i> cell cultures. The CMA-based SNP assay can identify the most prevalent resistance mediating mutations in the genes <i>rpoB</i>, <i>katG</i>, <i>embB</i>, and the promotor region of <i>inhA</i> within one hour.</p></div

Analysis of genomic DNA (g) and heat-inactivated cell culture material (c) from different <i>M</i>. <i>tuberculosis</i> strains.

<p>The target-specific genotypes (<i>rpoB</i>, <i>katG</i>, <i>embB</i>, promotor region of <i>inhA</i>) of analyzed strains are summarized in the table below. The test results are given as discrimination factors (y-axis) and present the average of three measurements. The x-axis shows the different mutant probes in the corresponding target region. The discrimination factors are given for the reaction of a mutation on its corresponding probe. All SNPs of the particular strain isolates could be identified precisely by a discrimination factor >1 which is characteristic for a mutation and by discrimination factor < 1 at probe positions which represented the wild type. No difference in reactivity was observed when inactivated crude culture material was applied compared to genomic DNA. The test results for all strains are available in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0183561#pone.0183561.s006" target="_blank">S4 Table</a>.</p