TY - JOUR T1 - Evolutionarily conserved network properties of intrinsically disordered proteins. JF - PLoS One Y1 - 2015 A1 - Rangarajan, Nivedita A1 - Kulkarni, Prakash A1 - Hannenhalli, Sridhar KW - Animals KW - Cluster Analysis KW - Databases, Protein KW - Drosophila KW - Drosophila Proteins KW - Evolution, Molecular KW - HUMANS KW - Intrinsically Disordered Proteins KW - Metabolic Networks and Pathways KW - Mice KW - Osmotic Pressure KW - Protein Interaction Maps KW - Saccharomyces cerevisiae KW - Saccharomyces cerevisiae Proteins AB -

BACKGROUND: Intrinsically disordered proteins (IDPs) lack a stable tertiary structure in isolation. Remarkably, however, a substantial portion of IDPs undergo disorder-to-order transitions upon binding to their cognate partners. Structural flexibility and binding plasticity enable IDPs to interact with a broad range of partners. However, the broader network properties that could provide additional insights into the functional role of IDPs are not known.

RESULTS: Here, we report the first comprehensive survey of network properties of IDP-induced sub-networks in multiple species from yeast to human. Our results show that IDPs exhibit greater-than-expected modularity and are connected to the rest of the protein interaction network (PIN) via proteins that exhibit the highest betweenness centrality and connect to fewer-than-expected IDP communities, suggesting that they form critical communication links from IDP modules to the rest of the PIN. Moreover, we found that IDPs are enriched at the top level of regulatory hierarchy.

CONCLUSION: Overall, our analyses reveal coherent and remarkably conserved IDP-centric network properties, namely, modularity in IDP-induced network and a layer of critical nodes connecting IDPs with the rest of the PIN.

VL - 10 CP - 5 M3 - 10.1371/journal.pone.0126729 ER - TY - JOUR T1 - CTCF binding site sequence differences are associated with unique regulatory and functional trends during embryonic stem cell differentiation JF - Nucleic Acids ResNucleic Acids ResNucleic Acids Res Y1 - 2014 A1 - Plasschaert, R. N. A1 - Vigneau, S. A1 - Tempera, I. A1 - Gupta, R. A1 - Maksimoska, J. A1 - Everett, L. A1 - Davuluri, R. A1 - Mamorstein, R. A1 - Lieberman, P. M. A1 - Schultz, D. A1 - Sridhar Hannenhalli A1 - Bartolomei, M. S. KW - *Gene Expression Regulation KW - *Regulatory Elements, Transcriptional KW - Animals KW - Binding Sites KW - Cell Differentiation/*genetics KW - Cells, Cultured KW - Embryonic Stem Cells/cytology/*metabolism KW - Mice KW - Nucleotide Motifs KW - Protein Binding KW - Repressor Proteins/*metabolism AB - CTCF (CCCTC-binding factor) is a highly conserved multifunctional DNA-binding protein with thousands of binding sites genome-wide. Our previous work suggested that differences in CTCF's binding site sequence may affect the regulation of CTCF recruitment and its function. To investigate this possibility, we characterized changes in genome-wide CTCF binding and gene expression during differentiation of mouse embryonic stem cells. After separating CTCF sites into three classes (LowOc, MedOc and HighOc) based on similarity to the consensus motif, we found that developmentally regulated CTCF binding occurs preferentially at LowOc sites, which have lower similarity to the consensus. By measuring the affinity of CTCF for selected sites, we show that sites lost during differentiation are enriched in motifs associated with weaker CTCF binding in vitro. Specifically, enrichment for T at the 18(th) position of the CTCF binding site is associated with regulated binding in the LowOc class and can predictably reduce CTCF affinity for binding sites. Finally, by comparing changes in CTCF binding with changes in gene expression during differentiation, we show that LowOc and HighOc sites are associated with distinct regulatory functions. Our results suggest that the regulatory control of CTCF is dependent in part on specific motifs within its binding site. VL - 42 SN - 1362-4962 (Electronic)
0305-1048 (Linking) N1 - Plasschaert, Robert N
Vigneau, Sebastien
Tempera, Italo
Gupta, Ravi
Maksimoska, Jasna
Everett, Logan
Davuluri, Ramana
Mamorstein, Ronen
Lieberman, Paul M
Schultz, David
Hannenhalli, Sridhar
Bartolomei, Marisa S
eng
K99AI099153/AI/NIAID NIH HHS/
P30 CA10815/CA/NCI NIH HHS/
R01 CA140652/CA/NCI NIH HHS/
R01-GM052880/GM/NIGMS NIH HHS/
R01CA140652/CA/NCI NIH HHS/
R01GM085226/GM/NIGMS NIH HHS/
R01HD042026/HD/NICHD NIH HHS/
T32GM008216/GM/NIGMS NIH HHS/
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
England
2013/10/15 06:00
Nucleic Acids Res. 2014 Jan;42(2):774-89. doi: 10.1093/nar/gkt910. Epub 2013 Oct 10. U2 - 3902912 J1 - Nucleic acids researchNucleic acids research ER - TY - JOUR T1 - Global secretome analysis identifies novel mediators of bone metastasis. JF - Cell Res Y1 - 2012 A1 - Blanco, Mario Andres A1 - LeRoy, Gary A1 - Khan, Zia A1 - Alečković, Maša A1 - Zee, Barry M A1 - Garcia, Benjamin A A1 - Kang, Yibin KW - Animals KW - Biomarkers, Tumor KW - Bone Neoplasms KW - Cell Line, Tumor KW - Collagen Type VI KW - Computational Biology KW - HUMANS KW - Mass Spectrometry KW - Mice KW - Neoplasms KW - Plasminogen Activators KW - Procollagen-Lysine, 2-Oxoglutarate 5-Dioxygenase KW - Proteome KW - proteomics KW - Salivary Cystatins AB -

Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.

VL - 22 CP - 9 M3 - 10.1038/cr.2012.89 ER - TY - JOUR T1 - Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization. JF - Nat Med Y1 - 2011 A1 - Korpal, Manav A1 - Ell, Brian J A1 - Buffa, Francesca M A1 - Ibrahim, Toni A1 - Blanco, Mario A A1 - Celià-Terrassa, Toni A1 - Mercatali, Laura A1 - Khan, Zia A1 - Goodarzi, Hani A1 - Hua, Yuling A1 - Wei, Yong A1 - Hu, Guohong A1 - Garcia, Benjamin A A1 - Ragoussis, Jiannis A1 - Amadori, Dino A1 - Harris, Adrian L A1 - Kang, Yibin KW - Animals KW - Cadherins KW - Cell Line, Tumor KW - Female KW - Gene Expression Profiling KW - Gene Expression Regulation, Neoplastic KW - HUMANS KW - Mass Spectrometry KW - Mice KW - Mice, Inbred BALB C KW - Microarray Analysis KW - MicroRNAs KW - Neoplasm Metastasis KW - Statistics, Nonparametric KW - Vesicular Transport Proteins AB -

Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin-dependent epithelial traits and Sec23a-mediated tumor cell secretome.

VL - 17 CP - 9 M3 - 10.1038/nm.2401 ER - TY - JOUR T1 - Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase. JF - Nature Y1 - 2011 A1 - Frezza, Christian A1 - Zheng, Liang A1 - Folger, Ori A1 - Rajagopalan, Kartik N A1 - MacKenzie, Elaine D A1 - Jerby, Livnat A1 - Micaroni, Massimo A1 - Chaneton, Barbara A1 - Adam, Julie A1 - Hedley, Ann A1 - Kalna, Gabriela A1 - Tomlinson, Ian P M A1 - Pollard, Patrick J A1 - Watson, Dave G A1 - Deberardinis, Ralph J A1 - Shlomi, Tomer A1 - Ruppin, Eytan A1 - Gottlieb, Eyal KW - Animals KW - Bilirubin KW - Cell Line KW - Cells, Cultured KW - Citric Acid Cycle KW - Computer simulation KW - Fumarate Hydratase KW - Fumarates KW - Genes, Lethal KW - Genes, Tumor Suppressor KW - Glutamine KW - Heme KW - Heme Oxygenase (Decyclizing) KW - Kidney Neoplasms KW - Leiomyomatosis KW - Mice KW - Mitochondria KW - Mutation KW - NAD KW - Neoplastic Syndromes, Hereditary KW - Skin Neoplasms KW - Uterine Neoplasms AB -

Fumarate hydratase (FH) is an enzyme of the tricarboxylic acid cycle (TCA cycle) that catalyses the hydration of fumarate into malate. Germline mutations of FH are responsible for hereditary leiomyomatosis and renal-cell cancer (HLRCC). It has previously been demonstrated that the absence of FH leads to the accumulation of fumarate, which activates hypoxia-inducible factors (HIFs) at normal oxygen tensions. However, so far no mechanism that explains the ability of cells to survive without a functional TCA cycle has been provided. Here we use newly characterized genetically modified kidney mouse cells in which Fh1 has been deleted, and apply a newly developed computer model of the metabolism of these cells to predict and experimentally validate a linear metabolic pathway beginning with glutamine uptake and ending with bilirubin excretion from Fh1-deficient cells. This pathway, which involves the biosynthesis and degradation of haem, enables Fh1-deficient cells to use the accumulated TCA cycle metabolites and permits partial mitochondrial NADH production. We predicted and confirmed that targeting this pathway would render Fh1-deficient cells non-viable, while sparing wild-type Fh1-containing cells. This work goes beyond identifying a metabolic pathway that is induced in Fh1-deficient cells to demonstrate that inhibition of haem oxygenation is synthetically lethal when combined with Fh1 deficiency, providing a new potential target for treating HLRCC patients.

VL - 477 CP - 7363 M3 - 10.1038/nature10363 ER - TY - JOUR T1 - Protein quantification across hundreds of experimental conditions. JF - Proc Natl Acad Sci U S A Y1 - 2009 A1 - Khan, Zia A1 - Bloom, Joshua S A1 - Garcia, Benjamin A A1 - Singh, Mona A1 - Kruglyak, Leonid KW - algorithms KW - Animals KW - Automatic Data Processing KW - Chromatography, Liquid KW - Databases, Factual KW - Fungal Proteins KW - HUMANS KW - Isotopes KW - Mice KW - Proteins KW - proteomics KW - Tandem Mass Spectrometry AB -

Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.

VL - 106 CP - 37 M3 - 10.1073/pnas.0904100106 ER - TY - JOUR T1 - Schistosoma mansoni: Microarray analysis of gene expression induced by host sex. JF - Exp Parasitol Y1 - 2008 A1 - Waisberg, M A1 - Lobo, F P A1 - Cerqueira, G C A1 - Passos, L K J A1 - Carvalho, O S A1 - El-Sayed, N M A1 - Franco, G R KW - Animals KW - Biomphalaria KW - Female KW - Gene expression KW - Host-Parasite Interactions KW - Male KW - Mice KW - Oligonucleotide Array Sequence Analysis KW - Reverse Transcriptase Polymerase Chain Reaction KW - RNA, Helminth KW - Schistosoma mansoni KW - Schistosomiasis mansoni KW - Sex Factors AB -

Schistosoma mansoni is a digenetic trematode and a human parasite responsible for high social and economic impact. Although some authors have studied the effect of host hormones on parasites, not much is known about the effects of host sex on gene expression in Schistosomes. In order to study gene transcripts associated with the host sex, we compared the gene expression profiles of both male and female unisexual adult S. mansoni parasites raised on either male or female hosts, using DNA microarrays. Our results show that host sex caused differential expression of at least 11 genes in female parasites and of 134 in male parasites. Of the differentially expressed genes in female worms, 10 were preferentially expressed in female worms from male mice, while of the 134 differentially expressed genes in male parasites, 79 (59%) were preferentially expressed in worms from female mice. Further investigation of the role of each of those genes will help understand better their importance in the pathogenesis of Schistosomiasis.

VL - 120 CP - 4 M3 - 10.1016/j.exppara.2008.09.005 ER - TY - JOUR T1 - X-ray crystal structure of the hypothetical phosphotyrosine phosphatase MDP-1 of the haloacid dehalogenase superfamily JF - BiochemistryBiochemistry Y1 - 2004 A1 - Peisach, Ezra A1 - J. Selengut A1 - Dunaway-Mariano, Debra A1 - Allen, Karen N. KW - Amino Acid Sequence KW - Animals KW - Binding Sites KW - Crystallography, X-Ray KW - HUMANS KW - Hydrogen-Ion Concentration KW - Hydrolases KW - Magnesium KW - Mice KW - Models, Molecular KW - Molecular Sequence Data KW - Phosphoprotein Phosphatases KW - Phosphotyrosine KW - Protein Phosphatase 1 KW - Protein Structure, Quaternary KW - Protein Structure, Tertiary KW - sequence alignment KW - Solvents KW - Substrate Specificity AB - The haloacid dehalogenase (HAD) superfamily is comprised of structurally homologous enzymes that share several conserved sequence motifs (loops I-IV) in their active site. The majority of HAD members are phosphohydrolases and may be divided into three subclasses depending on domain organization. In classes I and II, a mobile "cap" domain reorients upon substrate binding, closing the active site to bulk solvent. Members of the third class lack this additional domain. Herein, we report the 1.9 A X-ray crystal structures of a member of the third subclass, magnesium-dependent phosphatase-1 (MDP-1) both in its unliganded form and with the product analogue, tungstate, bound to the active site. The secondary structure of MDP-1 is similar to that of the "core" domain of other type I and type II HAD members with the addition of a small, 28-amino acid insert that does not close down to exclude bulk solvent in the presence of ligand. In addition, the monomeric oligomeric state of MDP-1 does not allow the participation of a second subunit in the formation and solvent protection of the active site. The binding sites for the phosphate portion of the substrate and Mg(II) cofactor are also similar to those of other HAD members, with all previously observed contacts conserved. Unlike other subclass III HAD members, MDP-1 appears to be equally able to dephosphorylate phosphotyrosine and closed-ring phosphosugars. Modeling of possible substrates in the active site of MDP-1 reveals very few potential interactions with the substrate leaving group. The mapping of conserved residues in sequences of MDP-1 from different eukaryotic organisms reveals that they colocalize to a large region on the surface of the protein outside the active site. This observation combined with the modeling studies suggests that the target of MDP-1 is most likely a phosphotyrosine in an unknown protein rather than a small sugar-based substrate. VL - 43 N1 - http://www.ncbi.nlm.nih.gov/pubmed/15461449?dopt=Abstract ER - TY - Generic T1 - Dynamic querying for pattern identification in microarray and genomic data T2 - 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings Y1 - 2003 A1 - Hochheiser, H. A1 - Baehrecke, E. H. A1 - Stephen M. Mount A1 - Shneiderman, Ben KW - Bioinformatics KW - data sets KW - Displays KW - dynamic querying KW - expression profiles KW - Frequency KW - Gene expression KW - genes KW - Genetics KW - genomic data KW - Genomics KW - linear ordered sequences KW - macromolecules KW - medical signal processing KW - Mice KW - Microarray KW - pattern identification KW - pattern recognition KW - premRNA splicing KW - Query processing KW - sequences KW - Signal processing KW - splicing KW - TimeSearcher AB - Data sets involving linear ordered sequences are a recurring theme in bioinformatics. Dynamic query tools that support exploration of these data sets can be useful for identifying patterns of interest. This paper describes the use of one such tool - timesearcher - to interactively explore linear sequence data sets taken from two bioinformatics problems. Microarray time course data sets involve expression levels for large numbers of genes over multiple time points. Timesearcher can be used to interactively search these data sets for genes with expression profiles of interest. The occurrence frequencies of short sequences of DNA in aligned exons can be used to identify sequences that play a role in the pre-mRNA splicing. Timesearcher can be used to search these data sets for candidate splicing signals. JA - 2003 International Conference on Multimedia and Expo, 2003. ICME '03. Proceedings PB - IEEE VL - 3 SN - 0-7803-7965-9 ER - TY - JOUR T1 - The transcription factor Eyes absent is a protein tyrosine phosphatase JF - NatureNature Y1 - 2003 A1 - Tootle, Tina L. A1 - Silver, Serena J. A1 - Davies, Erin L. A1 - Newman, Victoria A1 - Latek, Robert R. A1 - Mills, Ishara A. A1 - J. Selengut A1 - Parlikar, Beth E. W. A1 - Rebay, Ilaria KW - Amino Acid Motifs KW - Amino Acid Sequence KW - Animals KW - Antibodies, Phospho-Specific KW - Drosophila melanogaster KW - Drosophila Proteins KW - Embryonic Induction KW - eye KW - Eye Proteins KW - Gene Expression Regulation KW - Kinetics KW - Mice KW - Models, Molecular KW - Molecular Sequence Data KW - Mutation KW - Phosphorylation KW - Protein Conformation KW - Protein Tyrosine Phosphatases KW - Substrate Specificity KW - Transcription Factors AB - Post-translational modifications provide sensitive and flexible mechanisms to dynamically modulate protein function in response to specific signalling inputs. In the case of transcription factors, changes in phosphorylation state can influence protein stability, conformation, subcellular localization, cofactor interactions, transactivation potential and transcriptional output. Here we show that the evolutionarily conserved transcription factor Eyes absent (Eya) belongs to the phosphatase subgroup of the haloacid dehalogenase (HAD) superfamily, and propose a function for it as a non-thiol-based protein tyrosine phosphatase. Experiments performed in cultured Drosophila cells and in vitro indicate that Eyes absent has intrinsic protein tyrosine phosphatase activity and can autocatalytically dephosphorylate itself. Confirming the biological significance of this function, mutations that disrupt the phosphatase active site severely compromise the ability of Eyes absent to promote eye specification and development in Drosophila. Given the functional importance of phosphorylation-dependent modulation of transcription factor activity, this evidence for a nuclear transcriptional coactivator with intrinsic phosphatase activity suggests an unanticipated method of fine-tuning transcriptional regulation. VL - 426 N1 - http://www.ncbi.nlm.nih.gov/pubmed/14628053?dopt=Abstract ER - TY - JOUR T1 - MDP-1 is a new and distinct member of the haloacid dehalogenase family of aspartate-dependent phosphohydrolases JF - BiochemistryBiochemistry Y1 - 2001 A1 - J. Selengut KW - Amino Acid Motifs KW - Amino Acid Sequence KW - Animals KW - Aspartic Acid KW - Catalytic Domain KW - HUMANS KW - Hydrolases KW - Mice KW - Molecular Sequence Data KW - Multigene Family KW - Mutagenesis, Site-Directed KW - Phosphoprotein Phosphatases KW - Protein Structure, Tertiary KW - Protein Tyrosine Phosphatases KW - Rats KW - Saccharomyces cerevisiae KW - sequence alignment KW - Sequence Homology, Amino Acid AB - MDP-1 is a eukaryotic magnesium-dependent acid phosphatase with little sequence homology to previously characterized phosphatases. The presence of a conserved motif (Asp-X-Asp-X-Thr) in the N terminus of MDP-1 suggested a relationship to the haloacid dehalogenase (HAD) superfamily, which contains a number of magnesium-dependent acid phosphatases. These phosphatases utilize an aspartate nucleophile and contain a number of conserved active-site residues and hydrophobic patches, which can be plausibly aligned with conserved residues in MDP-1. Seven site-specific point mutants of MDP-1 were produced by modifying the catalytic aspartate, serine, and lysine residues to asparagine or glutamate, alanine, and arginine, respectively. The activity of these mutants confirms the assignment of MDP-1 as a member of the HAD superfamily. Detailed comparison of the sequence of the 15 MDP-1 sequences from various organisms with other HAD superfamily sequences suggests that MDP-1 is not closely related to any particular member of the superfamily. The crystal structures of several HAD family enzymes identify a domain proximal to the active site responsible for important interactions with low molecular weight substrates. The absence of this domain or any other that might perform the same function in MDP-1 suggests an "open" active site capable of interactions with large substrates such as proteins. This suggestion was experimentally confirmed by demonstration that MDP-1 is competent to catalyze the dephosphorylation of tyrosine-phosphorylated proteins. VL - 40 N1 - http://www.ncbi.nlm.nih.gov/pubmed/11601995?dopt=Abstract ER - TY - JOUR T1 - MDP-1: A novel eukaryotic magnesium-dependent phosphatase JF - BiochemistryBiochemistry Y1 - 2000 A1 - J. Selengut A1 - Levine, R. L. KW - Amino Acid Sequence KW - Animals KW - Catalysis KW - Cations KW - Chromatography, Affinity KW - Cloning, Molecular KW - Cysteine KW - Enzyme Inhibitors KW - Histidine KW - Hydrogen-Ion Concentration KW - Magnesium KW - Mice KW - Molecular Sequence Data KW - Phosphoprotein Phosphatases KW - Protein Phosphatase 1 KW - Rabbits KW - Sequence Analysis, Protein KW - Sequence Homology, Amino Acid KW - Substrate Specificity AB - We report here the purification, cloning, expression, and characterization of a novel phosphatase, MDP-1. In the course of investigating the reported acid phosphatase activity of carbonic anhydrase III preparations, several discrete phosphatases were discerned. One of these, a magnesium-dependent species of 18.6 kDa, was purified to homogeneity and yielded several peptide sequences from which the parent gene was identified by database searching. Although orthologous genes were identified in fungi and plants as well as mammalian species, there was no apparent homology to any known family of phosphatases. The enzyme was expressed in Escherichia coli with a fusion tag and purified by affinity methods. The recombinant enzyme showed magnesium-dependent acid phosphatase activity comparable to the originally isolated rabbit protein. The enzyme catalyzes the rapid hydrolysis of p-nitrophenyl phosphate, ribose-5-phosphate, and phosphotyrosine. The selectivity for phosphotyrosine over phosphoserine or phosphothreonine is considerable, but the enzyme did not show activity toward five phosphotyrosine-containing peptides. None of the various substrates assayed (including various nucleotide, sugar, amino acid and peptide phosphates, phosphoinositides, and phosphodiesters) exhibited K(M) values lower than 1 mM, and many showed negligible rates of hydrolysis. The enzyme is inhibited by vanadate and fluoride but not by azide, cyanide, calcium, lithium, or tartaric acid. Chemical labeling, refolding, dialysis, and mutagenesis experiments suggest that the enzymatic mechanism is not dependent on cysteine, histidine, or nonmagnesium metal ions. In recognition of these observations, the enzyme has been given the name magnesium-dependent phosphatase-1 (MDP-1). VL - 39 N1 - http://www.ncbi.nlm.nih.gov/pubmed/10889041?dopt=Abstract ER - TY - JOUR T1 - Small ribonucleoproteins from eukaryotes: structures and roles in RNA biogenesis. JF - Cold Spring Harb Symp Quant Biol Y1 - 1983 A1 - Steitz, J A A1 - Wolin, S L A1 - Rinke, J A1 - Pettersson, I A1 - Mount, S M A1 - Lerner, E A A1 - Hinterberger, M A1 - Gottlieb, E KW - Animals KW - Base Sequence KW - HeLa Cells KW - HUMANS KW - Mice KW - Molecular Weight KW - Nucleic Acid Conformation KW - Nucleic Acid Hybridization KW - Nucleoproteins KW - Ribonucleoproteins KW - Ribonucleoproteins, Small Nuclear KW - RNA Polymerase III KW - Transcription, Genetic VL - 47 Pt 2 ER - TY - JOUR T1 - Detection of alloantigens during preimplantation development and early trophoblast differentiation in the mouse by immunoperoxidase labeling. JF - J Exp Med Y1 - 1976 A1 - Searle, R F A1 - Sellens, M H A1 - Elson, J A1 - Jenkinson, E J A1 - Billington, W D KW - Animals KW - Binding Sites, Antibody KW - Blastocyst KW - Cell Differentiation KW - Cell Membrane KW - Embryo Implantation KW - Embryonic Development KW - Epitopes KW - Female KW - Histocompatibility Antigens KW - HLA Antigens KW - Horseradish Peroxidase KW - Mice KW - Mice, Inbred Strains KW - Pregnancy KW - Pregnancy, Animal KW - Trophoblasts AB -

An immunoperoxidase-labeling technique allowing visualization of antibody binding to the cell surface at the electron microscopical level has been employed an an analysis of H-2 and non-H-2 alloantigen expression on the early mouse embryo. The presence of non-H-2 antigenic determinants has been confirmed on eight-cell, morula, and blastocyst stages of development. Contrary to previous reports, however, low levels of H-2 antigen have also been detected on the blastocyst. This is the earliest stage at which H-2 has been shown to be expressed on the fertilized mouse egg and may reflect the greater resolution of the immunoperoxidase technique. Using two different models to study the critical peri-implantation stages, those of experimentally induced blastocyst activation and blastocyst outgrowth in vitro, it has been demonstrated that antigen loss occurs on the trophectoderm at the time of implantation, and that this is not necessarily dependent upon maternal influence. It is suggested that the loss may be an important factor in the prevention of maternal immune rejection during the establishment of the fetal allograft. The two major components of the early postimplantation conceptus display a striking differential in antigenic status. The embryonic sac shows a high degree of peroxidase labeling, while the ectoplacental cone trophoblast is unlabeled. These findings add support to the concept of antigenic neutrality of the early trophoblast and its role in the maintenance of a normal fetomaternal immunological equilibrium.

VL - 143 CP - 2 ER -