Natural history of SLC11 genes in vertebrates: tales from the fish world

Background  

The SLC11A1/Nramp1 and SLC11A2/Nramp2 genes belong to the SLC11/Nramp family of transmembrane divalent metal transporters, with SLC11A1 being associated with resistance to pathogens and SLC11A2 involved in intestinal iron uptake and transferrin-bound iron transport. Both members of the SLC11 gene family have been clearly identified in tetrapods; however SLC11A1 has never been documented in teleost fish and is believed to have been lost in this lineage during early vertebrate evolution. In the present work we characterized the SLC11 genes in teleosts and evaluated if the roles attributed to mammalian SLC11 genes are assured by other fish specific SLC11 gene members.     

Identification of a GH110 subfamily of alpha 1,3-galactosidases: novel enzymes for removal of the alpha 3Gal xenotransplantation antigen

In search of alpha-galactosidases with improved kinetic properties for removal of the immunodominant alpha1,3-linked galactose residues of blood group B antigens, we recently identified a novel prokaryotic family of alpha-galactosidases (CAZy GH110) with highly restricted substrate specificity and neutral pH optimum (Liu, Q. P., Sulzenbacher, G., Yuan, H., Bennett, E. P., Pietz, G., Saunders, K., Spence, J., Nudelman, E., Levery, S. B., White, T., Neveu, J. M., Lane, W. S., Bourne, Y., Olsson, M. L., Henrissat, B., and Clausen, H. (2007) Nat. Biotechnol. 25, 454-464). One member of this family from Bacteroides fragilis had exquisite substrate specificity for the branched blood group B structure Galalpha1-3(Fucalpha1-2)Gal, whereas linear oligosaccharides terminated by alpha1,3-linked galactose such as the immunodominant xenotransplantation epitope Galalpha1-3Galbeta1-4GlcNAc did not serve as substrates. Here we demonstrate the existence of two distinct subfamilies of GH110 in B. fragilis and thetaiotaomicron strains. Members of one subfamily have exclusive specificity for the branched blood group B structures, whereas members of a newly identified subfamily represent linkage specific alpha1,3-galactosidases that act equally well on both branched blood group B and linear alpha1,3Gal structures. We determined by one-dimensional (1)H NMR spectroscopy that GH110 enzymes function with an inverting mechanism, which is in striking contrast to all other known alpha-galactosidases that use a retaining mechanism. The novel GH110 subfamily offers enzymes with highly improved performance in enzymatic removal of the immunodominant alpha3Gal xenotransplantation epitope.     

Fluctuations in circumpolar seabird populations linked to climate oscillations

We found that synchronous fluctuations of two congeneric seabird species across the entire Arctic and sub-Arctic regions were associated with changes in sea surface temperatures (SST) that were linked to two climate shifts, in 1977 and again in 1989. As the SST changes linked to climate shifts were congruent at the scale of ocean basins, fluctuations of these species occurred similarly at continental or basin scale. Changes in colony sizes were examined for a decade following climate shifts. The magnitude of the SST shift was more important than its direction in determining the subsequent rate of population change. Seabirds declined when the SST shift was large and increased when the shift was small, although the effect differed between the Arctic-breeding species and the more temperate-breeding congener. The Arctic species, Thick-billed Murre ( Uria lomvia ) increased most rapidly when SST warmed slightly, while the temperate species, Common Murre ( Uria aalge ) showed most rapid increase with moderate cooling. Both showed negative trends with large temperature shifts in either direction. This pattern was replicated during both climate oscillations. Negative population trends in seabirds presumably indicate the alteration of underlying food webs. Hence, similar widespread fluctuations in response to climate shifts are likely for other ecosystem components (marine mammals, fish, and invertebrates).     

Mollusk shell formation: mapping the distribution of organic matrix components underlying a single aragonitic tablet in nacre

Control over mineral formation in mollusk shells is exerted by the macromolecules of the organic matrix. Using histochemical methods, we mapped the carboxylates and sulfates of proteins and polysaccharides on the surfaces of decalcified interlamellar matrices from the nacreous shell layer of the cephalopod Nautilus pompilius, expanding upon an earlier study by Crenshaw and Ristedt [Crenshaw, M.A., Ristedt, H., 1976. The histochemical localization of reactive groups in septal nacre from Nautilus pompilius. In: Watabe, N., Wilbur, K.M. (Ed.), The Mechanisms of Mineralization in the Invertebrates and Plants. University of South Carolina Press, Colombia, pp. 355-367]. We observed four different zones underlying a single crystal: (1) a central spot rich in carboxylates; (2) a central ring-shaped area rich in sulfates; (3) an area between the central nucleation region and the imprint periphery containing carboxylates, and (4) the intertabular matrix, rich in carboxylates and sulfates. We also mapped matrix functional groups on the nacreous matrix surfaces of the bivalve Atrina rigida, but did not identify well-defined zones. Immuno-mapping of the constituents of the aragonite-nucleating protein fraction from Atrina nacre showed that these macromolecules are located both in the intertabular matrix and in the center of the crystal imprints for both Atrina and Nautilus matrix surfaces. Their presence at the latter location is consistent with their purported role in aragonite nucleation. The observed differentiation in the distribution of matrix components and their functional groups shows that the different stages of single crystal growth are highly controlled by the matrix.     

Characterization of a novel biochemical abnormality in galactosemia: deficiency of glycolipids containing galactose or N-acetylgalactosamine and accumulation of precursors in brain and lymphocytes

Classic galactosemia, an inborn error of human galactose metabolism, is characterized by a deficiency of the enzyme galactose-1-phosphate uridyltransferase (GALT). The current model for the pathophysiology of this disease ascribes most of its symptoms to the toxicity of intracellular galactose-1-phosphate (Gal-1-P), one of the substrates of GALT which accumulates in the untreated disease state. Recently, a reduction in the intracellular concentration of UDP-Gal (uridine diphosphogalactose), one of the products of GALT, has been described in treated galactosemic patients. We investigated whether galactosemic patients might also have reduced amounts of those macromolecules that depend on UDP-Gal for their biosynthesis. We report a reduction in glycolipids that contain either galactose or its derivative N-acetylgalactosamine and an accumulation of the precursors to these compounds in the brain of a neonate with galactosemia. We also found an imbalance in glycolipids in galactosemic lymphoblasts. This novel biochemical abnormality observed in galactosemic patients is not addressed by dietary galactose-restriction therapy and could explain some of the chronic neurologic and other complications of galactosemia.     

Novel fucolipids accumulating in human adenocarcinoma. III. A hybridoma antibody (FH6) defining a human cancer-associated difucoganglioside (VI3NeuAcV3III3Fuc2nLc6)

A new fucoganglioside, 6B, which accumulates in human colonic adenocarcinoma but is absent in normal colonic mucosa, was isolated from a monosialoganglioside fraction of colonic adenocarcinomas. The structure of this ganglioside was identified as shown below by methylation analysis, direct probe mass spectrometry, and enzymatic degradation followed by examination of the degradation products with specific monoclonal antibodies. (formula; see text) The hybridoma (FH6) secreting a monoclonal IgM antibody directed to this glycolipid was selected by reactivity of the antibody with this ganglioside and lack of reactivity with other glycolipids having a closely related structure, such as sialosyllactoneotetraosylceramide (IV3NeuAcnLc4), sialosyllactofucopentaosy(III)ceramide (IV3NeuAcIII3FucnLc4), sialosyllactofucopentaosy(II)ceramide (sialosyl-Lea glycolipid; IV3NeuAcIII4FucLc4), and 6C fucoganglioside (sialosyl 2 leads to 6 fucoganglioside; VI6NeuAcIII3FucnLc6). The antibody was highly reactive with a large variety of human cancer cells, but was less reactive or did not react with a variety of normal cells.     

Isolation and characterization of novel glycolipids with blood group A-related structures: galactosyl-A and sialosylgalactosyl-A

Two glycosphingolipids with the following novel structures have been isolated from human blood cells and characterized by NMR, direct probe mass spectrometry, fast atom bombardment-mass spectrometry, and methylation analysis: (Formula: see text). Both structure i and structure ii are characterized by substitution of beta-galactosyl or sialosyl-beta-galactosyl residue at the terminal alpha-GalNAc residue of blood group A determinant and are therefore specific products associated with the blood group A phenotype.     

The pause in firing of a primary muscle spindle at the transition between dynamic and static stretch: A mathematical model

A mathematical model to offer an explanation of the pause in firing of a primary muscle spindle at the transition between dynamic and static stretch is suggested. It is proposed that the firing frequency is proportional to a generator current at the site of the transduction (presumably the five terminal endings) and that the receptor potential is a version of this current filtered by the passive cable properties of the nerve between site of transduction and site of measurement.A mathematical expression is derived for the receptor potential from data in the literature. From this and an equivalent circuit of the nerve, an expression for the generator current is derived.This work was partially supported by National Institutes of Health Training Grant, Presbyterian-St. Luke's Hospital grant-in-aid and National Science Foundation. It was done in partial fulfillment of the requirements for the degree of Doctor of Philosophy (HBN) at the University of Illinois at the Medical Center.     

Pre-erythrocytic stages of plasmodia. Role of specific and nonspecific factors

Protection against pre-erythrocytic stages of malaria is possible as demonstrated by the generation of resistance after immunization with irradiated sporozoites. However, mechanisms involved are more numerous and intricate than previously believed and it progressively appears that the role of the presumed target, the sporozoite, might be negligible compared with that of the hepatic stage. The comparative use of in vivo and in vitro models clearly demonstrates that the intrahepatocytic parasite can be the target of antibodies, cytokines, phagocytic and cytotoxic cells, nonspecific factors--mechanisms in part induced by the previous or subsequent developmental stages.     

DNA polymerase η mutational signatures are found in a variety of different types of cancer

DNA polymerase (pol) η is a specialized error-prone polymerase with at least two quite different and contrasting cellular roles: to mitigate the genetic consequences of solar UV irradiation, and promote somatic hypermutation in the variable regions of immunoglobulin genes. Misregulation and mistargeting of pol η can compromise genome integrity. We explored whether the mutational signature of pol η could be found in datasets of human somatic mutations derived from normal and cancer cells. A substantial excess of single and tandem somatic mutations within known pol η mutable motifs was noted in skin cancer as well as in many other types of human cancer, suggesting that somatic mutations in A:T bases generated by DNA polymerase η are a common feature of tumorigenesis. Another peculiarity of pol ηmutational signatures, mutations in YCG motifs, led us to speculate that error-prone DNA synthesis opposite methylated CpG dinucleotides by misregulated pol η in tumors might constitute an additional mechanism of cytosine demethylation in this hypermutable dinucleotide.