Evidence of a Cadmium-Thionein and the Glycine Cleavage System in Oxytricha granulifera

ABSTRACT. This work presents the further purification of a Cd-linking protein in Oxytricha granulifera by reverse-phase chromatography. This protein contains 25% cysteine and no aromatic amino acid. it may be considered as a chelatin with some similarity to metallothioneins. During the purification of another Cd-linking compound, we were able to demonstrate that the H protein precursor of glycine cleavage is present in Oxytricha. This is the first finding of the presence of this system in Protozoa.     

Fluorescence in situ hybridization with specific oligonucleotide rRNA probes distinguishes the sibling species Stylonychia lemnae and Stylonychia mytilus (Ciliophora, Spirotrichea)

Based on morphological and morphogenetic characters alone, the sibling species Stylonychia lemnae and Stylonychia mytilus, members of the Stylonychia mytilus complex, can hardly be distinguished. However, biochemical investigations of the isoenzyme pattern of different enzymes showed a distinct differentiation between these two species. In the last few years, fluorescence in situ hybridization (FISH) techniques have become a suitable and reliable tool for identification and differentiation of closely related species of protozoa, such as ciliates. To distinguish the sibling species, a set of specific oligonucleotide probes were developed. In the present study, the SSU rDNA of 7 clones of Stylonychia lemnae and 13 clones of Stylonychia mytilus, isolated from different geographic regions, were sequenced. Comparing all SSU rDNA sequences of both species, only one single difference within the whole gene was detected. Based on this difference, a set of two oligonucleotide probes, targeting the SSU rRNA of each species (Stylonychia mytilus and Stylonychia lemnae) was designed. These probes were successfully tested by applying the FISH techniques on preserved cells of different clones of both species.     

Isolation and Partial Purification of Cadmium-Binding Protein from Roots of the Grass Agrostis gigantea

A cadmium-binding protein was isolated from roots of the grass Agrostis gigantea Roth. Heat-stable proteins were chromatographed on the anion exchanger QAE-Sephadex A-25. The major cadmium fraction was purified further by gel filtration on Sephadex G-75 in 1 molar KCl buffer. The resulting protein preparation was light brown, had an apparent molecular weight of 3700, contained 29% cysteine and close to 4 gram atoms cadmium/mole. The cadmium:cysteine ratio was 1:2.7. Spectroscopic measurements indicated cadmium-thiolate coordination. The roots produced the metallothionein-like protein when they were exposed to cadmium for 7 days.     

Resistance to Cadmium Ions and Formation of a Cadmium-Binding Complex in Various Wild-Type Yeasts

The resistance to cadmium ions (Cd-resistance) and possibleformation of cadmium-binding complexes were examined in eightdifferent wild-type yeasts. Saccharomyces exiguus, Pichia farinosa,Torulaspora delbrueckii and Schizosaccharomyces octosporus exhibitedpartial Cd-resistance, as compared to the Cd-resistant strain301N and the Cu-resistant but Cd-sensitive strain X2180-1B ofSaccharomyces cerevisiae. Saccharomyces carlsbergensis, Pichiamogii, Zygosaccharomyces rouxii and Kluyveromyces lactis wereall Cd-sensitive. The partially Cd-sensitive species, with theexception of S. exiguus, accumulated Cd²⁺ ions in the cytoplasmicfraction to varying extents. This fraction from S. octosporusincluded a Cd-binding complex that contained (     

A New Subspecies of Oxytricha granulifera (Hypotrichia: Oxytrichidae) from Mexico,with Notes on its Morphogenesis and Phylogenetic Position

The genus Oxytricha Bory de Saint‐Vincent in Lamouroux, Bory de Saint‐Vincent and Deslongchamps, 1824 comprises about 38 species distributed worldwide and has been considered to be a nonmonophyletic group. Based on living observations, protargol preparations, and a small subunit ribosomal RNA (SSU rRNA) gene sequence, we describe a new subspecies Oxytricha granulifera chiapasensis n. subsp. This new taxon is morphologically characterized by undulating membranes basically in a Stylonychia‐pattern, six dorsal kineties, size in vivo ca. 60–120 × 20–40 μm, 21–30 right and 21–31 left marginal cirri, 22–29 adoral membranelles, and spherical cortical granules arranged in longitudinal rows on the dorsal side. In terms of the SSU rRNA gene sequence, the new subspecies differs from populations of O. granulifera from GENBANK by 7–35 nucleotides. Phylogenetic analyses showed that Oxytricha granulifera gene sequences were nested into three groups, with the new subspecies included in one of them. Oxytricha granulifera chiapasensis n. subsp. is different from Oxytricha granulifera granulifera Foissner and Adam, 1983 and Oxytricha granulifera quadricirrata Blatterer and Foissner, 1988 based on: (i) undulating membranes in Stylonychia‐pattern, (ii) formation of a sixth dorsal kinety during morphogenesis, (iii) the adoral membranelles number, and (iv) inhabiting freshwater habitats.     

Macronuclear and micronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1α in Stylonychia lemnae

The micronuclear and macronuclear configurations of a gene encoding the protein synthesis elongation factor EF 1 alpha in the hypotrich ciliate Stylonychia lemnae were compared. The two sequences are generally colinear. The coding sequence of the micronuclear gene is, however, interrupted by a 64 bp insert flanked by a 2 bp direct repeat in a gene region which is moderately conserved among EF 1 alpha genes of different organisms. The insertion site is distinct from known intron positions in eukaryotic EF 1 alpha genes. The insert sequence shows inverted repeats at its ends and thus exhibits typical features of an internal eliminated sequence (IES). Comparison with other such sequences in the related organism Oyxtricha nova shows that the IES falls into a new group of such elements. The macronuclear gene exhibits a strikingly limited codon usage, which cannot be simply explained by the overall base composition of the DNA but probably also relates to the very high copy number of the macronuclear gene and the putative high amount of the gene product.     

The Structure and Development of the Dorsal Bristle Complex of Oxytricha fallax and Stylonychia pustulata*

SYNOPSIS. Oxytricha fallax and Stylonychia pustulata possess 6 rows of dorsal bristle units. Each dorsal bristle unit consists of a pair of kinetosomes; the anterior kinetosome has a cilium and the posterior kinetosome a ciliary stub. The kinetosome pair, located at the bottom of a cortical pit surrounding the cilium and ciliary stub, is surrounded by an asymmetrical fibrillar mass. Future rows 1-4 are formed from 2 sets of primordia originating within mature dorsal rows 1-3. Rows 5 and 6 originate from the anterior regions of both right marginal cirral primordia. Old dorsal bristle units utilized in formation of primordia are presumably maintained in the new rows of the proter and opisthe; those outside the primordia are resorbed. The morphogenetic pattern of the Oxytrichidae is similar to those of the Urostylidae and Holostichidae, but quite different from that of the Euplotidae.     

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea)

DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.     

植物防御素调控水稻镉积累的新机制

镉是我国农产品的主要重金属污染物之一。随着我国土壤重金属污染问题日益突出, 包括稻米在内的农产品重金属超标时常发生。如何防控重金属在作物可食部位的积累, 在保证农产品安全的同时将农田重金属进行移除修复, 已成为我国农业生产急需解决的问题。最近, 中科院上海生命科学院植物生理生态所龚继明研究组和中国水稻所钱前研究组克隆到1个特异调控镉在水稻(Oryza sativa)叶片中积累的主效QTL基因CAL1。CAL1编码1个植物防御素类似蛋白, 通过与镉进行螯合, 将镉从维管束木质部薄壁细胞中分泌出来, 进入木质部参与长距离转运, 从而定向调控镉在水稻叶片等营养器官的积累而不影响籽粒镉的积累。该研究加深了人们对重金属镉在植物体内的转运和再分配机理的认识, 同时也为培育秸秆镉高积累而籽粒镉含量达标的“修复型”水稻品种提供有价值的新基因。研究成果具有重要的理论意义和应用价值。     

Structures, basins, and energies: a deconstruction of the Protein Coil Library

Globular proteins adopt complex folds, composed of organized assemblies of alpha-helix and beta-sheet together with irregular regions that interconnect these scaffold elements. Here, we seek to parse the irregular regions into their structural constituents and to rationalize their formative energetics. Toward this end, we dissected the Protein Coil Library, a structural database of protein segments that are neither alpha-helix nor beta-strand, extracted from high-resolution protein structures. The backbone dihedral angles of residues from coil library segments are distributed indiscriminately across the phi,psi map, but when contoured, seven distinct basins emerge clearly. The structures and energetics associated with the two least-studied basins are the primary focus of this article. Specifically, the structural motifs associated with these basins were characterized in detail and then assessed in simple simulations designed to capture their energetic determinants. It is found that conformational constraints imposed by excluded volume and hydrogen bonding are sufficient to reproduce the observed ,psi distributions of these motifs; no additional energy terms are required. These three motifs in conjunction with alpha-helices, strands of beta-sheet, canonical beta-turns, and polyproline II conformers comprise approximately 90% of all protein structure.     

Binding linkage in a telomere DNA-protein complex at the ends of Oxytricha nova chromosomes

Alpha and beta protein subunits of the telomere end binding protein from Oxytricha nova (OnTEBP) combine with telomere single strand DNA to form a protective cap at the ends of chromosomes. We tested how protein-protein interactions seen in the co-crystal structure relate to DNA binding through use of fusion proteins engineered as different combinations of domains and subunits derived from OnTEBP. Joining alpha and beta resulted in a protein that bound single strand telomere DNA with high affinity (K(D-DNA)=1.4 nM). Another fusion protein, constructed without the C-terminal protein-protein interaction domain of alpha, bound DNA with 200-fold diminished affinity (K(D-DNA)=290 nM) even though the DNA-binding domains of alpha and beta were joined through a peptide linker. Adding back the alpha C-terminal domain as a separate protein restored high-affinity DNA binding. The binding behaviors of these fusion proteins and the native protein subunits are consistent with cooperative linkage between protein-association and DNA-binding equilibria. Linking DNA-protein stability to protein-protein contacts at a remote site may provide a trigger point for DNA-protein disassembly during telomere replication when the single strand telomere DNA must exchange between a very stable OnTEBP complex and telomerase.     

人类蛋白质结构互作网络——结构域对网络拓扑与蛋白质功能的影响

高通量的蛋白质互作数据与结构域互作数据的出现,使得在蛋白质组学领域内研究人类蛋白质结构互作网络,进一步揭示蛋白质结构与功能间的潜在关系成为可能.蛋白质上广泛分布的结构域被认为是蛋白质结构、功能以及进化的基本功能单元.然而,结合蛋白质的结构信息(例如蛋白质结构域数目、长度和覆盖率等)来研究这些表象后的内部机制仍然面临着挑战.将蛋白质分为单结构域蛋白质与多结构域蛋白质,并进一步结合蛋白质互作信息与结构域互作信息构建了人类蛋白质结构互作网络;通过与人类蛋白质互作网络进行比较,研究了人类蛋白质结构互作网络的特殊结构特征;对于单结构域蛋白质与多结构域蛋白质,分别进行了功能富集分析、功能离散度分析以及功能一致性分析等.结果发现,将结构域互作信息综合考虑进来后,人类蛋白质结构互作网络可以提供更多的单纯的蛋白质互作网络无法提供的细节信息,揭示蛋白质互作网络的复杂性.     

Isolation of PGP 9.5, a New Human Neurone-Specific Protein Detected by High-Resolution Two-Dimensional Electrophoresis

Protein gene product (PGP) 9.5 is a new brain-specific protein originally detected by high-resolution two-dimensional electrophoresis of the soluble proteins of human brain and other organs. We have purified this protein from human brain and raised a rabbit antihuman PGP 9.5 antiserum. The protein has a monomer molecular weight of approximately 27,000 and is present in brain at concentrations at least 50 times greater than in other organs. Immunoperoxidase labelling has localised PGP 9.5 to neurones in the human cerebral cortex with no evidence of staining of glial elements. PGP 9.5 is estimated to be present in brain at concentrations of 200-500 micrograms/g wet weight and represents a major protein component of neuronal cytoplasm. This new neurone-specific cytoplasmic marker may prove useful in studies of neuronal development and in the detection of neuronal damage in disease of the nervous system.     

Isolation from Cholinergic Synapses of a Protein That Binds to Membranes in a Calcium-Dependent Manner

A protein that binds to membranes in a calcium-dependent manner between calcium concentrations of 10(-5) and 10(-6) M has been isolated in large amounts (20 mg/kg tissue) from the entirely cholinergic electric organ of Torpedo marmorata. The protein bound reversibly to membrane fractions in a calcium-specific and saturable manner. The protein also bound to lipids isolated from Torpedo electric organ and to clathrin-coated vesicles prepared from pig brain. The protein bound to a Triton X-100-sensitive site. It had an apparent subunit molecular weight of 32,000 by polyacrylamide gel electrophoresis and of 35,900 by amino acid analysis; a broad isoelectric range of 4.8 to 5.5; and 27% of its amino acids after hydrolysis were observed to be aspartic and glutamic acids. Synaptosomes derived from electric organ were enriched in the protein which is probably localised within the nerve ending. It was localised in the synaptic region of the electric organ by means of immunofluorescence. In the electric lobe, discrete patches of fluorescence were seen within the cell bodies that innervate the electric organ. The protein may be involved in the recognition of membranes within the cholinergic neurone. Proteins with similar purification properties were found in all tissues investigated so far, and polypeptides of subunit molecular weight 32,000 were identified in bovine adrenal medulla and guinea pig brain synaptosomes.     

Isolation of a Thiamine-binding Protein from Rice Germ and Distribution of Similar Proteins

A thiamine-binding protein was purified from rice germ (Oryza sativa L.) by extraction, salting-out with ammonium sulfate, and column chromatography. From the results of molecular mass, K_d and B_max values for thiamine-binding, binding specificity for thiamine phosphates and analog, the protein was suggested to be identical to the thiamine-binding protein in rice bran. The thiamine-binding protein w as more efficiently purified from rice germ than from rice bran. The protein was rich in glutamic acid (and/or glutamine) and glycine. The protein did not show immunological similarity to thiamine-binding proteins in buckwheat and sesame seeds. However proteins similar to the thiamine-binding protein from rice germ existed in gramineous seeds. They were suggested to have thiamine-binding activity and to be of the same molecular mass as the thiamine-binding protein.     

Cadmium inhibits delta-aminolevulinate dehydratase from rat lung in vitro: interaction with chelating and antioxidant agents

The effect of cadmium (Cd(2+)) on delta-aminolevulinate dehydratase (delta-ALA-D) activity from rat lung in vitro was investigated. delta-ALA-D activity, a parameter for metal intoxication, has been reported as a target of Cd(2+) in different tissues. The protective effect of monotherapies with dithiol chelating (meso-2,3-dimercaptosuccinic acid (DMSA) and 2,3-dimercaptopropane-1-sulfonic acid (DMPS)) or antioxidant agents (ascorbic acid, diphenyl diselenide (PhSe)(2), and N-acetylcysteine (NAC)) was evaluated. The effect of a combined therapy (dithiol chelatingxantioxidant agent) was also studied. Zinc chloride (ZnCl(2)) and dithiothreitol (DTT) were used to investigate the mechanisms involved in cadmium, chelating and antioxidant effects on delta-ALA-D activity. Cadmium inhibited rat lung delta-ALA-D activity at low concentrations. DTT (3mM), but not ZnCl(2) (100microM), protected the inhibition of enzyme activity caused by Cd(2+). Chelating agents were not effective in restoring the enzyme activity. DMPS and DMSA presented inhibitory effect on enzyme activity. DTT restored the inhibition caused by both chelating agents, but ZnCl(2) restored only the inhibitory effect induced by DMSA. These compounds caused a marked potentiation of delta-ALA-D inhibition induced by Cd(2+). ZnCl(2) did not restore inhibition of enzyme activity caused by Cd(2+) plus chelating agents. Conversely, DTT restored the inhibition induced by Cd(2+)/DMSA, but not by Cd(2+)/DMPS. Antioxidants were not effective in ameliorating delta-ALA-D inhibition induced by Cd(2+), whereas ascorbic acid potentiated the enzyme inhibition induced by this metal. A combined effect of Cd(2+)xDMPSx(PhSe)(2) and Cd(2+)xDMPSxNAC was observed. There was no combined effect of Cd(2+)xchelatorxantioxidants when DMSA was used. This study demonstrated that Cd(2+)inhibited delta-ALA-D activity and chelating and antioxidant agents, alone or combined, did not restore the enzyme activity. In contrast, these compounds potentiated the inhibition induced by Cd(2+) in rat lung.