Diversity of olfactomedin proteins in the sea urchin

Calcium-ligand variants of the myocilin olfactomedin propeller selected from invertebrate phyla reveal cross-talk with N-terminal blade and surface helices

Olfactomedins are a family of modular proteins found in multicellular organisms that all contain five-bladed β-propeller olfactomedin (OLF) domains. In support of differential functions for the OLF propeller, the available crystal structures reveal that only some OLF domains harbor an internal calcium-binding site with ligands derived from a triad of residues. For the myocilin OLF domain (myoc-OLF), ablation of the ion-binding site (triad Asp, Asn, Asp) by altering the coordinating residues affects the stability and overall structure, in one case leading to misfolding and glaucoma. Bioinformatics analysis reveals a variety of triads with possible ion-binding characteristics lurking in OLF domains in invertebrate chordates such as Arthropoda (Asp-Glu-Ser), Nematoda (Asp-Asp-His) and Echinodermata (Asp-Glu-Lys). To test ion binding and to extend the observed connection between ion binding and distal structural rearrangements, consensus triads from these phyla were installed in the myoc-OLF. All three protein variants exhibit wild-type-like or better stability, but their calcium-binding properties differ, concomitant with new structural deviations from wild-type myoc-OLF. Taken together, the results indicate that calcium binding is not intrinsically destabilizing to myoc-OLF or required to observe a well ordered side helix, and that ion binding is a differential feature that may underlie the largely elusive biological function of OLF propellers.

Olfactomedin domain-containing proteins: evolution, functional divergence, expression patterns and damaging SNPs

Olfactomedin domain-containing proteins appear to facilitate neurodevelopment, cell adhesion, intercellular interactions, and protein-protein interactions, and the disruption of their expression will lead to dramatic developmental perturbations and lethality. The aim of the present work was to study how these genes evolved in metazoans and diverged after their duplication as well as to characterize their expression profiles and detrimental mutations. We conducted an exhaustive survey of olfactomedin domain-containing genes in genomic databases, identifying 235 olfactomedin-like (OLF) proteins in 29 representative species covering all the main metazoan lineages. Phylogenetic analyses allowed us to define nine different subfamilies of OLF genes, and subfamily IX, which specifically includes two immunoglobulin domains, was identified for the first time in arthropods. Functional divergence analysis suggested that the function of this arthropod-specific OLF subfamily might have diverged from that of other subfamilies. Expression pattern analysis of OLF genes in humans and rats showed that human OLF genes tended to be highly expressed in the brain, while rat OLF genes were inclined to be expressed in the ovary and brain. We used the SIFT and PolyPhen servers in dbNSFP to distinguish deleterious mutations from neutral mutations for each member of the OLF gene family. The results showed that OLFML2B contains the most destructive SNPs (up to 61), while none of the mutations in OLFM2, OLFM4 and LPHN2 were predicted to be harmful. Taken together, these findings may not only enhance understanding of the phylogenetic relationships of the OLF family but also aid future studies on OLF protein regulation of nervous system development and immune function.

Methods for collection, handling, and analysis of sea urchin coelomocytes

Sea urchin coelomocytes can be collected in large numbers from adult sea urchins of the species, Strongylocentrotus purpuratus, which typically has 12-40mL of coelomic fluid. Coelomocytes are used for analysis of immune reactions and immune gene expression in addition to basic functions of cells, in particular for understanding structure and modifications of the cytoskeleton in phagocytes. The methods described here include coelomocyte isolation, blocking the clotting reaction, establishing and maintaining primary cultures, separation of different types of coelomocytes into fractions, processing live coelomocytes for light microscopy, fixation and staining for light and electron microscopy, analysis of coelomocyte populations by flow cytometry, and sorting single cells for more detailed follow-up analyses including transcriptomics or genomic characteristics. These methods are provided to make working with coelomocytes accessible to researchers who are unfamiliar with these cells and perhaps to aid others who have worked extensively with invertebrate cells.

Extraordinary Diversity of Immune Response Proteins among Sea Urchins: Nickel-Isolated Sp185/333 Proteins Show Broad Variations in Size and Charge

Effective protection against pathogens requires the host to produce a wide range of immune effector proteins. The Sp185/333 gene family, which is expressed by the California purple sea urchin Strongylocentrotus purpuratus in response to bacterial infection, encodes a highly diverse repertoire of anti-pathogen proteins. A subset of these proteins can be isolated by affinity to metal ions based on multiple histidines, resulting in one to four bands of unique molecular weight on standard Western blots, which vary depending on the individual sea urchin. Two dimensional gel electrophoresis (2DE) of nickel-isolated protein samples followed by Western blot was employed to detect nickel-isolated Sp185/333 (Ni-Sp185/333) proteins and to evaluate protein diversity in animals before and after immune challenge with marine bacteria. Ni-Sp185/333 proteins of the same molecular weight on standard Western blots appear as a broad complex of variants that differ in pI on 2DE Western blots. The Ni-Sp185/333 protein repertoire is variable among animals, and shows a variety of changes among individual sea urchins in response to immune challenges with both the same and different species of bacteria. The extraordinary diversity of the Ni-Sp185/333 proteins may provide significant anti-pathogen capabilities for sea urchins that survive solely on innate immunity.

Olfactomedin proteins: central players in development and disease

Olfactomedin proteins are characterized by a conserved domain of \texorpdfstring~\textasciitilde250 amino acids corresponding to the olfactomedin archetype first discovered in olfactory neuroepithelium. They arose early in evolution and occur throughout the animal kingdom. In mice and humans olfactomedin proteins comprise a diverse array of glycoproteins, many of which are critical for early development and functional organization of the nervous system as well as hematopoiesis. Olfactomedin domains appear to facilitate protein-protein interactions, intercellular interactions, and cell adhesion. Several members of the family have been implicated in various common diseases, notably myocilin in glaucoma and OLFM4 in cancer. This review highlights this important, hitherto understudied family of proteins.

Stem cell marker olfactomedin 4: critical appraisal of its characteristics and role in tumorigenesis

Olfactomedin 4 (OLFM4), a member of the olfactomedin domain-containing proteins, is a glycoprotein with molecular weight of approximately 64 kDa. The protein is a "robust marker" of Lgr5+ stem cells and has been localised to mitochondria, nuclei and cell membranes. The bulk of OLFM4 exists in a polymeric form which is held together by disulfide bonds and carbohydrate interactions. Earlier studies revealed that the protein binds to lectins and cadherins, and facilitates cell-cell adhesion. Recent data demonstrated that the protein possesses several hallmarks of carcinogenesis. OLFM4 has also been purported to be an inducible resistance factor to apoptotic stimuli such as radiation and anticancer drugs. Here, we review its synonyms and classification, gene structure, protein structure, intracellular and tissue distribution, adhesive and antiapoptotic; mitotic; migratory and cell cycle regulatory characteristics. We also critically evaluate recent advances in understanding of the transcriptional regulation of OLFM4 and its upstream signalling pathways with special emphasis on carcinogenesis and outline future perspectives in the field.

In-vitro study of the activity of ciprofloxacin alone and in combination against strains of Pseudomonas aeruginosa with multiple antibiotic resistance

Ciprofloxacin appears to have useful activity against Pseudomonas aeruginosa. We have studied its in-vitro activity against ten strains of Ps. aeruginosa with multiple antibiotic resistance. We have confirmed that ciprofloxacin is very active against Ps. aeruginosa with minimal inhibitory concentrations ranging from 0.07 to 0.7 mg/l. Killing curves show ciprofloxacin to be rapidly bactericidal with no regrowth after 24 h. Checkerboard studies with ciprofloxacin in combination with gentamicin, azlocillin and ceftazidime show no consistent interaction. These studies suggest that ciprofloxacin should prove a useful antibiotic in treating infections caused by multiresistant Ps. aeruginosa.