A gene family of silicon transporters

Silica-precipitating Peptides from Diatoms

Two silica-precipitating peptides, silaffin-1A(1) and-1A(2), both encoded by the sil1 gene from the diatom Cylindrotheca fusiformis, were extracted from cell walls and purified to homogeneity. The chemical structures were determined by protein chemical methods combined with mass spectrometry. Silaffin-1A(1) and -1A(2) consist of 15 and 18 amino acid residues, respectively. Each peptide contains a total of four lysine residues, which are all found to be post-translationally modified. In silaffin-1A(2) the lysine residues are clustered in two pairs in which the epsilon-amino group of the first residue is linked to a linear polyamine consisting of 5 to 11 N-methylated propylamine units, whereas the second lysine is converted to epsilon-N,N-dimethyllysine. Silaffin-1A(1) contains only a single lysine pair exhibiting the same structural features. One of the two remaining lysine residues was identified as epsilon-N,N,N-trimethyl-delta-hydroxylysine, a lysine derivative containing a quaternary ammonium group. The fourth lysine residue again is linked to a long-chain polyamine. Silaffin-1A(1) is the first peptide shown to contain epsilon-N,N,N-trimethyl-delta-hydroxylysine. In vitro, both peptides precipitate silica nanospheres within seconds when added to a monosilicic acid solution.

Molecular phylogeny as a basis for the classification of transport proteins from bacteria, archaea and eukarya

Although enzymes catalyzing chemical reactions have long been classified according to the system developed by the Enzyme Commission (EC), no comparable system has been developed or proposed for transport proteins catalyzing transmembrane vectorial reactions. We here propose a comprehensive system, designated the Transport Commission (TC) system, based both on function and phylogeny. The TC system initially categorizes permeases according to mode of transport and energy coupling mechanism, and each category is assigned a one-component TC number (W). The secondary level of classification corresponds to the phylogenetic family (or superfamily) to which a particular permease is assigned, and each family is assigned a two-component TC number (W.X). The third level of classification refers to the phylogenetic cluster within a family (or the family within a superfamily) to which the permease belongs, and each cluster receives a three-component TC number (W.X.Y). Finally, the last level of categorization is based on substrate specificity and polarity of transport, and each entry is assigned a four component TC number (W.X.Y.Z). This system is based on the observation that mode of transport and energy coupling mechanism are fundamental properties of transport systems that very seldom transcend familial lines, but substrate specificity, being readily alterable by point mutations, is a superficial characteristic that often transcends familial lines. The proposed system has the potential to include all known permeases for which sequence data are available and has the flexibility to accommodate the multitude of permeases likely to be revealed by future genome sequencing and biochemical analysis. Major conclusions resulting from our classification efforts are described. The classification system, which will be continuously updated, is available on our World Wide Web site (http:/(/)www-biology.ucsd.edu/ approximately msaier/transport/titlepage.html).

Eukaryotic transmembrane solute transport systems

A comprehensive classification system for transmembrane molecular transporters has been proposed. This system is based on (i) mode of transport and energy-coupling mechanism, (ii) protein phylogenetic family, (iii) phylogenetic cluster, and (iv) substrate specificity. The proposed "Transport Commission" (TC) system is superficially similar to that implemented decades ago by the Enzyme Commission for enzymes, but it differs from the latter system in that it uses phylogenetic and functional data for classification purposes. Very few families of transporters include members that do not function exclusively in transport. Analyses reported reveal that channels, primary carriers, secondary carriers (uni-, sym-, and antiporters), and group translocators comprise distinct categories of transporters, and that transport mode and energy coupling are relatively immutable characteristics. By contrast, substrate specificity and polarity of transport are often readily mutable. Thus, with very few exceptions, a unified family of transporters includes members that function by a single transport mode and energy-coupling mechanism although a variety of substrates may be transported with either inwardly or outwardly directed polarity. The TC system allows cross-referencing according to substrates transported and protein sequence database accession numbers. Thus, familial assignments of newly sequenced transport proteins are facilitated. In this article I examine families of transporters that are eukaryotic specific. These families include (i) channel proteins, mostly from animals; (ii) facilitators and secondary active transport carriers; (iii) a few ATP-dependent primary active transporters; and (iv) transporters of unknown mode of action or energy-coupling mechanism. None of the several ATP-independent primary active transport energy-coupling mechanisms found in prokaryotes is represented within the eukaryotic-specific families. The analyses reported provide insight into transporter families that may have arisen in eukaryotes after the separation of eukaryotes from archaea and bacteria. On the basis of the reported analyses, it is suggested that the horizontal transfer of genes encoding transport proteins between eukaryotes and members of the other two domains of life occurred very infrequently during evolutionary history.

Di[(hydroxyalkyl)dimethylammonium] tris[benzene-1,2-diolato(2–)]silicates and their germanium analogs: syntheses, crystal structure analyses, and NMR studies

Treatment of Si(OMe)4 with three molar equivalents of 1,2-C6H4(OH)2 (= 1,2-dihydroxybenzene) and two molar equivalents of HO(CH2)nNMe2 (n = 2, 3) in acetonitrile at room temperature yields the λ6Si-silicates (HO(CH2)nNMe2H)2(SiL3) (5: n = 2; 6: n = 3; L2– = 1,2-C6H4(O)22– (= benzene-1,2-diolato(2–))). The analogous λ6Ge-germanates (HO(CH2)nNMe2H)2(GeL3) (7: n = 2; 8: n = 3) were synthesized analogously starting from Ge(OMe)4. Compounds 5·2CH3CN and 6-8 were structurally characterized by single-crystal X-ray diffraction. In addition, aqueous solutions of the Si/Ge analogs 5/7 and 6/8 were studied by NMR spectroscopy. The title compounds may be regarded as model systems for the transport and storage of silicon in biological systems and as tools to investigate biosilification.Key words: hexacoordinate silicon, hexacoordinate germanium, silicon biochemistry

Xenopus oocytes as an expression system for plant transporters

The Xenopus oocyte provides a powerful system for the expression and characterisation of plant membrane proteins. Many different types of plant membrane proteins have been expressed and characterised using this system. As there are already several general reviews on the methodology for oocyte expression of channel proteins, we have summarised the particular advantages and disadvantages of using the system for the characterisation of plant cotransporter proteins. As an example of how the system can be used to identify transporters, we describe evidence for a low affinity nitrate transporter in oocytes injected with poly(A) RNA extracted from nitrate-induced barley roots. Furthermore, we describe evidence that the expression of some transporters in oocytes can modify the properties of endogenous membrane proteins. We conclude that although care must be taken in the interpretation of results and in choosing appropriate controls for experiments, oocyte expression is an excellent tool which will have an important role in characterising plant membrane proteins.

SILICON

Silicon is present in plants in amounts equivalent to those of such macronutrient elements as calcium, magnesium, and phosphorus, and in grasses often at higher levels than any other inorganic constituent. Yet except for certain algae, including prominently the diatoms, and the Equisetaceae (horsetails or scouring rushes), it is not considered an essential element for plants. As a result it is routinely omitted from formulations of culture solutions and considered a nonentity in much of plant physiological research. But silicon-deprived plants grown in conventional nutrient solutions to which silicon has not been added are in many ways experimental artifacts. They are often structurally weaker than silicon-replete plants, abnormal in growth, development, viability, and reproduction, more susceptible to such abiotic stresses as metal toxicities, and easier prey to disease organisms and to herbivores ranging from phytophagous insects to mammals. Many of these same conditions afflict plants in silicon-poor soils-and there are such. Taken together, the evidence is overwhelming that silicon should be included among the elements having a major bearing on plant life.

Silicatein filaments and subunits from a marine sponge direct the polymerization of silica and silicones in vitro

Nanoscale control of the polymerization of silicon and oxygen determines the structures and properties of a wide range of siloxane-based materials, including glasses, ceramics, mesoporous molecular sieves and catalysts, elastomers, resins, insulators, optical coatings, and photoluminescent polymers. In contrast to anthropogenic and geological syntheses of these materials that require extremes of temperature, pressure, or pH, living systems produce a remarkable diversity of nanostructured silicates at ambient temperatures and pressures and at near-neutral pH. We show here that the protein filaments and their constituent subunits comprising the axial cores of silica spicules in a marine sponge chemically and spatially direct the polymerization of silica and silicone polymer networks from the corresponding alkoxide substrates in vitro, under conditions in which such syntheses otherwise require either an acid or base catalyst. Homology of the principal protein to the well known enzyme cathepsin L points to a possible reaction mechanism that is supported by recent site-directed mutagenesis experiments. The catalytic activity of the "silicatein" (silica protein) molecule suggests new routes to the synthesis of silicon-based materials.

Boron stimulates embryonic trout growth

Boron is present in our soil, water and air. Cyanobacteria require it for nitrogen fixation, and vascular plants require it for the formation of cell walls and membranes. I report here how boron affects the growth of embryonic rainbow trout (Oncorhynchus mykiss). Fertilized ovum from the Mt. Whitney rainbow trout strain were incubated at (12.5 degreesC) in Type 1 ASTM ultrapure grade water supplemented with boric acid (99.5% purity) during the 1995 and 1997 spawning seasons. Boron concentrations of the incubation solutions were determined by direct measurement using the curcumin procedure or inductively coupled plasma-mass spectrometry. In the 1995 study boron ranged from 1 to 936 micromol/L. Ca, Na and Mg salts were included in the incubation solutions to approximate concentrations in natural water. In the 1997 study fertilized eggs were incubated in ultrapure water supplemented with boric acid alone over a range from 2.2 to 90.6 micromol/L. The 1995 study used 144 embryos per B concentration and the 1997 study used 96 embryos per B concentration. Growth and teratogenicity were evaluated at the eye, hatch and 2-wk posthatch developmental stages. Boron stimulated growth in a dose-dependent manner in both studies (P < 0.001), and exposure was associated with an increase in B body concentration (P < 0.05). No teratogenic or microbicidal effects were apparent. These results are consistent with those expected of an element essential for vertebrate development. J. Nutr. 2488-2493, 128: 1998

Silicatein alpha: cathepsin L-like protein in sponge biosilica

Earth's biota produces vast quantities of polymerized silica at ambient temperatures and pressures by mechanisms that are not understood. Silica spicules constitute 75% of the dry weight of the sponge Tethya aurantia, making this organism uniquely tractable for analyses of the proteins intimately associated with the biosilica. Each spicule contains a central protein filament, shown by x-ray diffraction to exhibit a highly regular, repeating structure. The protein filaments can be dissociated to yield three similar subunits, named silicatein alpha, beta, and gamma. The molecular weights and amino acid compositions of the three silicateins are similar, suggesting that they are members of a single protein family. The cDNA sequence of silicatein alpha, the most abundant of these subunits, reveals that this protein is highly similar to members of the cathepsin L and papain family of proteases. The cysteine at the active site in the proteases is replaced by serine in silicatein alpha, although the six cysteines that form disulfide bridges in the proteases are conserved. Silicatein alpha also contains unique tandem arrays of multiple hydroxyls. These structural features may help explain the mechanism of biosilicification and the recently discovered activity of the silicateins in promoting the condensation of silica and organically modified siloxane polymers (silicones) from the corresponding silicon alkoxides. They suggest the possibility of a dynamic role of the silicateins in silicification of the sponge spicule and offer the prospect of a new synthetic route to silica and siloxane polymers at low temperature and pressure and neutral pH.