Silicate mineralogy of basalts at DSDP Leg 54 Holes

Basalts drilled from the East Pacific Rise, OCP Ridge, and Siqueiros fracture zone during Leg 54 are texturally diverse. Dolerites are equigranular at Sites 422 and 428 and porphyritic, with phenocrysts of plagioclase (An69.73) and Ca-rich clinopyroxene (Ca42Mg48Fe10) at Site 427. The East Pacific Rise lavas and some of those from the OCP Ridge are fine-grained and porphyritic. The majority of the large crystals are clustered skeletal glomerocrysts of plagioclase An64-77), together with olivine (Fo80-87), Ca-rich clinopyroxene, or both. Euhedral phenocrysts of plagioclase, together with olivine, Carich clinopyroxene, and Cr-Al spinel in some cases, occur in most of the fine-grained lavas. These phenocrysts are small (maximum dimension <1 mm in all but one sample), sparse (combined modal amount <1% in all samples), and distinctive from the megacrysts which characterize many ocean-floor lavas. In two East Pacific Rise lavas, zoned plagioclase (An83 cores) is the sole phenocryst phase. In other porphyritic lavas from all the main East Pacific Rise and OCP Ridge units drilled during Leg 54, the plagioclase phenocrysts contain cores of bytownite (An79-87) surrounded by more-sodic feldspar (An67-77). Core/rim relationships vary from continuous normal zoning, through discontinuous zoning, to extensive resorption of the calcic cores in some samples. The compositions of the plagioclase calcic cores are systematically related to those of the glomerophyric plagioclase and olivine in the lavas containing them. Furthermore, only one compositional population of calcic cores occurs in each rock. The possible causes of these relationships are far from clear. Magma mixing, although superficially applicable, is inconsistent with important aspects of the phenocryst mineralogy of these particular lavas. A more satisfactory model to explain both phenocryst zoning and rapid glomerocryst growth immediately before extrusion may be constructed by postulating influx of water into the upwelling magmas within Layer 3 of the oceanic crust beneath the East Pacific Rise, and subsequent loss of part of this water during effervescence within feeder dykes between Layer 3 and the ocean floor. It is shown that this model is fully consistent with published data on water and carbon dioxide contents and ratios in the pillow-margin glasses, vesicles, and phenocryst inclusions of ocean-floor basalts. The evidence for the precipitation of plagioclase- dominated crystalline assemblages from these magmas in the upper part of Layer 3 is concordant with recent geophysically based modeling of the structure of the East Pacific Rise. Calcium-rich clinopyroxenes in dolerites from the OCP Ridge and Siqueiros fracture zone show radial, oscillatory, and sector-zoning. In Sample 428A-5-2 (Piece 5a), the compositional trends resulting from this zoning closely resemble those of the pyroxenes in some lunar lavas. The controls on crystallization of interstitial pigeonite - epitaxial upon augite - in this rock are discussed. Both sector-zoning of the augite and nucleation of pigeonite within microvolumes of magma with a low Ca(Mg + Fe) ratio appear to be important factors.

Whole rock and Cr-rich spinel geochemistry of ODP Legs 152 and 163 and DSDP Hole 38-338 samples

Coring during Ocean Drilling Program and Deep Sea Drilling Project Legs 163, 152, 104, 81, and 38 recovered sequences of altered basalt from North Atlantic seaward-dipping reflector sequences (SDRS) erupted during the initial rifting of Greenland from northern Europe and likely associated with excessive mantle temperatures caused by an impacting mantle plume head. Cr-rich spinel is found abundantly as inclusions and groundmass crystals within the olivine-rich lavas of Hole 917A (Leg 152) cored into the Southeast Greenland SDRS, but only rarely as inclusions within plagioclase in the lavas of the Vøring Plateau SDRS, and it is absent from other cored SDRS lavas from the Rockall Plateau and Southeast Greenland. Eruptive melt compositions determined from inferred, thermodynamically-defined, spinel-melt exchange equilibria indicate that the most primitive melts represented by Hole 917A basalts have Mg/(Mg + Fe2+) at least as high as 0.70 and approach near-primary mantle melt compositions. In contrast, Cr-rich spinels from Hole 338 (Leg 38) lavas on the Vøring Plateau SDRS give evidence for melt with Mg/(Mg + Fe2+) only as high as 0.64. This study underlines that primitive melts similar to those from Hole 917A comprise only a small fraction of the eruptive North Atlantic SDRS melts, and that most SDRS basalts were, in fact, too evolved to have precipitated Cr-rich spinel, with true melt Mg/(Mg + Fe2+) likely below 0.60. The evolved nature of the SDRS basalts implies large amounts of fractionation at the base of the crust or deep within it, consistent with seismic results that indicate an abnormally thick Layer 3 underlying the SDRS.

Fluctuating silicate:nitrate ratios and coastal plankton food webs

Marine diatoms require dissolved silicate to form an external shell, and their growth becomes Si-limited when the atomic ratio of silicate to dissolved inorganic nitrogen (Si:DIN) approaches 1:1, also known as the “Redfield ratio.” Fundamental changes in the diatom-to-zooplankton-to-higher trophic level food web should occur when this ratio falls below 1:1 and the proportion of diatoms in the phytoplankton community is reduced. We quantitatively substantiate these predictions by using a variety of data from the Mississippi River continental shelf, a system in which the Si:DIN loading ratio has declined from around 3:1 to 1:1 during this century because of land-use practices in the watershed. We suggest that, on this shelf, when the Si:DIN ratio in the river decreases to less than 1:1, then (i) copepod abundance changes from >75% to <30% of the total mesozooplankton, (ii) zooplankton fecal pellets become a minor component of the in situ primary production consumed, and (iii) bottom-water oxygen consumption rates become less dependent on relatively fast-sinking (diatom-rich) organic matter packaged mostly as zooplankton fecal pellets. This coastal ecosystem appears to be a pelagic food web dynamically poised to be either a food web composed of diatoms and copepods or one with potentially disruptive harmful algal blooms. The system is directed between these two ecosystem states by Mississippi River water quality, which is determined by land-use practices far inland.

A zinc finger directory for high-affinity DNA recognition

We have used two monovalent phage display libraries containing variants of the Zif268 DNA-binding domain to obtain families of zinc fingers that bind to alterations in the last 4 bp of the DNA sequence of the Zif268 consensus operator, GCG TGGGCG. Affinity selection was performed by altering the Zif268 operator three base pairs at a time, and simultaneously selecting for sets of 16 related DNA sequences. In this way, only four experiments were required to select for all possible 64 combinations of DNA triplet sequences. The results show that (i) for high-affinity DNA binding in the range observed for the Zif268 wild-type complex (Kd = 0.5–5 nM), finger 1 specifically requires the arginine at the carboxy terminus of its recognition helix that forms a bidentate hydrogen-bond with the guanine base (G) in the crystal structure of Zif268 complexed to its DNA operator sequence GCG TGG GCG; (ii) when the guanine base (G) is replaced by A, C, or T, a lower-affinity family (Kd ⩾ 50 nM) can be detected that shows an overall tendency to bind G-rich DNA; (iii) the residues at position 2 on the finger 2 recognition helix do not appear to interact strongly with the complementary 5′ base in the finger 1 binding site; and (iv) unexpected substitutions at the amino terminus of finger 1 can occasionally result in specificity for the 3′ base in the finger 1 binding site. A DNA recognition directory was constructed for high-affinity zinc fingers that recognize all three bases in a DNA triplet for seven sequences of the type GNN. Similar approaches may be applied to other zinc fingers to broaden the scope of the directory.

Ultrastructural localization of zinc transporter-3 (ZnT-3) to synaptic vesicle membranes within mossy fiber boutons in the hippocampus of mouse and monkey

Zinc transporter-3 (ZnT-3), a member of a growing family of mammalian zinc transporters, is expressed in regions of the brain that are rich in histochemically reactive zinc (as revealed by the Timm’s stain), including entorhinal cortex, amygdala, and hippocampus. ZnT-3 protein is most abundant in the zinc-enriched mossy fibers that project from the dentate granule cells to hilar and CA3 pyramidal neurons. We show here by electron microscopy that ZnT-3 decorates the membranes of all clear, small, round synaptic vesicles (SVs) in the mossy fiber boutons of both mouse and monkey. Furthermore, up to 60–80% of these SVs contain Timm’s-stainable zinc. The coincidence of ZnT-3 on the membranes of SVs that accumulate zinc, and its homology with known zinc transporters, suggest that ZnT-3 is responsible for the transport of zinc into SVs, and hence for the ability of these neurons to release zinc upon excitation.

Treble clef finger—a functionally diverse zinc-binding structural motif

Detection of similarity is particularly difficult for small proteins and thus connections between many of them remain unnoticed. Structure and sequence analysis of several metal-binding proteins reveals unexpected similarities in structural domains classified as different protein folds in SCOP and suggests unification of seven folds that belong to two protein classes. The common motif, termed treble clef finger in this study, forms the protein structural core and is 25–45 residues long. The treble clef motif is assembled around the central zinc ion and consists of a zinc knuckle, loop, β-hairpin and an α-helix. The knuckle and the first turn of the helix each incorporate two zinc ligands. Treble clef domains constitute the core of many structures such as ribosomal proteins L24E and S14, RING fingers, protein kinase cysteine-rich domains, nuclear receptor-like fingers, LIM domains, phosphatidylinositol-3-phosphate-binding domains and His-Me finger endonucleases. The treble clef finger is a uniquely versatile motif adaptable for various functions. This small domain with a 25 residue structural core can accommodate eight different metal-binding sites and can have many types of functions from binding of nucleic acids, proteins and small molecules, to catalysis of phosphodiester bond hydrolysis. Treble clef motifs are frequently incorporated in larger structures or occur in doublets. Present analysis suggests that the treble clef motif defines a distinct structural fold found in proteins with diverse functional properties and forms one of the major zinc finger groups.

Exploring the DNA-binding specificities of zinc fingers with DNA microarrays

A key step in the regulation of networks that control gene expression is the sequence-specific binding of transcription factors to their DNA recognition sites. A more complete understanding of these DNA–protein interactions will permit a more comprehensive and quantitative mapping of the regulatory pathways within cells, as well as a deeper understanding of the potential functions of individual genes regulated by newly identified DNA-binding sites. Here we describe a DNA microarray-based method to characterize sequence-specific DNA recognition by zinc-finger proteins. A phage display library, prepared by randomizing critical amino acid residues in the second of three fingers of the mouse Zif268 domain, provided a rich source of zinc-finger proteins with variant DNA-binding specificities. Microarrays containing all possible 3-bp binding sites for the variable zinc fingers permitted the quantitation of the binding site preferences of the entire library, pools of zinc fingers corresponding to different rounds of selection from this library, as well as individual Zif268 variants that were isolated from the library by using specific DNA sequences. The results demonstrate the feasibility of using DNA microarrays for genome-wide identification of putative transcription factor-binding sites.

Initiation of (-) strand DNA synthesis from tRNA(3Lys) on lentiviral RNAs: implications of specific HIV-1 RNA-tRNA(3Lys) interactions inhibiting primer utilization by retroviral reverse transcriptases.

Initiation of minus (-) strand DNA synthesis was examined on templates containing R, U5, and primer-binding site regions of the human immunodeficiency virus type 1 (HIV-1), feline immunodeficiency virus (FIV), and equine infectious anemia virus (EIAV) genomic RNA. DNA synthesis was initiated from (i) an oligoribonucleotide complementary to the primer-binding sites, (ii) synthetic tRNA(3Lys), and (iii) natural tRNA(3Lys), by the reverse transcriptases of HIV-1, FIV, EIAV, simian immunodeficiency virus, HIV type 2 (HIV-2), Moloney murine leukemia virus, and avian myeloblastosis virus. All enzymes used an oligonucleotide on wild-type HIV-1 RNA, whereas only a limited number initiated (-) strand DNA synthesis from either tRNA(3Lys). In contrast, all enzymes supported efficient tRNA(3Lys)-primed (-) strand DNA synthesis on the genomes of FIV and EIAV. This may be in part attributable to the observation that the U5-inverted repeat stem-loop of the EIAV and FIV genomes lacks an A-rich loop shown with HIV-1 to interact with the U-rich tRNA anticodon loop. Deletion of this loop in HIV-1 RNA, or disrupting a critical loop-loop complex by tRNA(3Lys) extended by 9 nt, restored synthesis of HIV-1 (-) strand DNA from primer tRNA(3Lys) by all enzymes. Thus, divergent evolution of lentiviruses may have resulted in different mechanisms to use the same host tRNA for initiation of reverse transcription.

Identification and characterization of a RING zinc finger gene (C-RZF) expressed in chicken embryo cells.

To identify changes in gene expression that occur in chicken embryo brain (CEB) cells as a consequence of their binding to the extracellular matrix molecule cytotactin/tenascin (CT/TN), a subtractive hybridization cloning strategy was employed. One of the cDNA clones identified was predicted to encode 381 amino acids and although it did not resemble any known sequences in the nucleic acid or protein data bases, it did contain the sequence motif for the cysteine-rich C3HC4 type of zinc finger, also known as a RING-finger. This sequence was therefore designated the chicken-RING zinc finger (C-RZF). In addition to the RING-finger, the C-RZF sequence also contained motifs for a leucine zipper, a nuclear localization signal, and a stretch of acidic amino acids similar to the activation domains of some transcription factors. Southern analysis suggested that C-RZF is encoded by a single gene. Northern and in situ hybridization analyses of E8 chicken embryo tissues indicated that expression of the C-RZF gene was restricted primarily to brain and heart. Western analysis of the nuclear and cytoplasmic fractions of chicken embryo heart cells and immunofluorescent staining of chicken embryo cardiocytes with anti-C-RZF antibodies demonstrated that the C-RZF protein was present in the nucleus. The data suggest that we have identified another member of the RING-finger family of proteins whose expression in CEB cells may be affected by CT/TN and whose nuclear localization and sequence motifs predict a DNA-binding function in the nucleus.

In vivo and in vitro characterization of the B1 and B2 zinc-binding domains from the acute promyelocytic leukemia protooncoprotein PML.

Acute promyelocytic leukemia (APL) has been ascribed to a chromosomal translocation event which results in a fusion protein comprising the PML protein and retinoic acid receptor alpha. PML is normally a component of a nuclear multiprotein complex which is disrupted in the APL disease state. Here, two newly defined cysteine/histidine-rich protein motifs called the B-box (B1 and B2) from PML have been characterized in terms of their effect on PML nuclear body formation, their dimerization, and their biophysical properties. We have shown that both peptides bind Zn2+, which induces changes in the peptides' structures. We demonstrate that mutants in both B1 and B2 do not form PML nuclear bodies in vivo and have a phenotype that is different from that observed in the APL disease state. Interestingly, these mutations do not affect the ability of wild-type PML to dimerize with mutant proteins in vitro, suggesting that the B1 and B2 domains are involved in an additional interaction central to PML nuclear body formation. This report in conjunction with our previous work demonstrates that the PML RING-Bl/B2 motif plays a fundamental role in formation of a large multiprotein complex, a function that may be common to those unrelated proteins which contain the motif.

The leukemia-associated-protein (LAP) domain, a cysteine-rich motif, is present in a wide range of proteins, including MLL, AF10, and MLLT6 proteins.

We have identified and further characterized a Caenorhabditis elegans gene, CEZF, that encodes a protein with substantial homology to the zinc finger and leucine zipper motifs of the human gene products AF10, MLLT6, and BR140. The first part of the zinc finger region of CEZF has strong similarity to the corresponding regions of AF10 (66%) and MLLT6 (64%) at the cDNA level. As this region is structurally different from previously described zinc finger motifs, sequence homology searches were done. Twenty-five other proteins with a similar motif were identified. Because the functional domain of this motif is potentially disrupted in leukemia-associated chromosomal translocations, we propose the name of leukemia-associated protein (LAP) finger. On the basis of these comparisons, the LAP domain consensus sequence is Cys1-Xaa1-2-Cys2-Xaa9-21-Cys3-Xaa2-4 -Cys4-Xaa4-5-His5-Xaa2-Cys6-Xaa12-46 - Cys7-Xaa2-Cys8, where subscripted numbers represent the number of amino acid residues. We review the evidence that this motif binds zinc, is the important DNA-binding domain in this group of regulatory proteins, and may be involved in leukemogenesis.