1
|
Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling. Proc Natl Acad Sci U S A 2017; 114:E1336-E1344. [PMID: 28167777 DOI: 10.1073/pnas.1615351114] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To elucidate the dynamic features of a biologically relevant large-scale reaction network, we constructed a computational model of minimal protein synthesis consisting of 241 components and 968 reactions that synthesize the Met-Gly-Gly (MGG) peptide based on an Escherichia coli-based reconstituted in vitro protein synthesis system. We performed a simulation using parameters collected primarily from the literature and found that the rate of MGG peptide synthesis becomes nearly constant in minutes, thus achieving a steady state similar to experimental observations. In addition, concentration changes to 70% of the components, including intermediates, reached a plateau in a few minutes. However, the concentration change of each component exhibits several temporal plateaus, or a quasi-stationary state (QSS), before reaching the final plateau. To understand these complex dynamics, we focused on whether the components reached a QSS, mapped the arrangement of components in a QSS in the entire reaction network structure, and investigated time-dependent changes. We found that components in a QSS form clusters that grow over time but not in a linear fashion, and that this process involves the collapse and regrowth of clusters before the formation of a final large single cluster. These observations might commonly occur in other large-scale biological reaction networks. This developed analysis might be useful for understanding large-scale biological reactions by visualizing complex dynamics, thereby extracting the characteristics of the reaction network, including phase transitions.
Collapse
|
2
|
Orlov DN, Orlov NY. Nucleoside diphosphate kinase and GTP-binding proteins. Possible mechanisms of coupling. Biophysics (Nagoya-shi) 2008. [DOI: 10.1134/s000635090806002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
3
|
Orlov NI, Ishijima Y, Orlov DN, Orlova TG, Bursteĭn EA, Kimura N. Investigation of chimerical and tagged forms of recombinant rat nucleoside diphosphate kinases alpha and beta. Interaction with rhodopsin-transducin complex and thermal stability. BIOCHEMISTRY (MOSCOW) 2007; 72:835-42. [PMID: 17922640 DOI: 10.1134/s0006297907080044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
To elucidate the physicochemical basis of differences between the isoforms of mammalian multifunctional nucleoside diphosphate kinase (NDP), we investigated the recombinant rat homohexameric NDP kinases alpha and beta, consisting of highly homologous alpha or beta subunits of 152 residues each and differing only in variable regions V1 and V2, and their chimerical forms (NDP kinase alpha(1-130)beta(131-152) and NDP kinase beta(1-130)alpha(131-152)) and tagged derivatives (NDP kinase HA-alpha(1-130)beta(131-152), NDP kinase HA-beta(1-130)alpha(131-152), and NDP kinase HA-beta). The thermal stability of these proteins and the ability of some of them to interact with the rhodopsin-transducin (R*Gt) complex have been studied. It was found that NDP kinase alpha, NDP kinase alpha(1-130)beta(131-152), and NDP kinase HA-alpha(1-130)beta(131-152) were similar in their thermal stability (T(1/2) = 61-63 degrees C). NDP kinase beta, NDP kinase beta(1-130)alpha(131-152), NDP kinase HA-beta(1-130)alpha(131-152), and NDP kinase HA-beta were inactivated at a lower temperature (T(1/2) = 51-54 degrees C). NDP kinase HA-alpha(1-130)beta(131-152) interacted with the R*Gt complex in the same manner as NDP kinase alpha, whereas the interaction of NDP kinase HA-beta(1-130)alpha(131-152) and NDP kinase beta with the photoreceptor membranes under the same conditions was very weak. It is suggested that the variability of the region V1 is a structural basis for the multifunctionality of NDP kinase hexamers in the cell.
Collapse
Affiliation(s)
- N Ia Orlov
- Tokyo Metropolitan Institute of Gerontology, Itabashi-ku, Tokyo, 173-0015, Japan.
| | | | | | | | | | | |
Collapse
|
4
|
Amrein L, Barraud P, Daniel JY, Pérel Y, Landry M. Expression patterns of nm23 genes during mouse organogenesis. Cell Tissue Res 2005; 322:365-78. [PMID: 16082520 DOI: 10.1007/s00441-005-0036-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Accepted: 06/14/2005] [Indexed: 01/21/2023]
Abstract
Nucleoside di-phosphate kinase enzyme (NDPK) isoforms, encoded by the nm23 family of genes, may be involved in various cellular differentiation and proliferation processes. We have therefore analyzed the expression of nm23-M1, -M2, -M3, and -M4 during embryonic mouse development. In situ hybridization data has revealed the differential expression of nm23 mRNA during organogenesis. Whereas nm23-M1 and -M3 are preferentially expressed in the nervous and sensory systems, nm23-M2 mRNA is found ubiquitously. Irrespective of the developmental state studied, nm23-M4 mRNA is only expressed at low levels in a few embryonic organs. In the cerebellum and cerebral cortex, nm23-M1, -M2, and -M3 are present in the neuronal differentiation layer, whereas nm23-M4 mRNA is distributed in the proliferating layer. Thus, nm23 mRNA is differentially expressed, and the diverse NDPK isoforms are sequentially involved in various developmental processes.
Collapse
Affiliation(s)
- Lilian Amrein
- EA DRED 483, Laboratoire de Biologie de la Différenciation et du Développement, Université Victor Ségalen, Bordeaux 2, 33 076, Bordeaux Cedex, France
| | | | | | | | | |
Collapse
|
5
|
Rao RV, Poksay KS, Castro-Obregon S, Schilling B, Row RH, del Rio G, Gibson BW, Ellerby HM, Bredesen DE. Molecular components of a cell death pathway activated by endoplasmic reticulum stress. J Biol Chem 2003; 279:177-87. [PMID: 14561754 DOI: 10.1074/jbc.m304490200] [Citation(s) in RCA: 121] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Alterations in Ca2+ homeostasis and accumulation of misfolded proteins in the endoplasmic reticulum (ER) cause ER stress that ultimately leads to programmed cell death. Recent studies have shown that ER stress triggers programmed cell death via an alternative intrinsic pathway of apoptosis that, unlike the intrinsic pathway described previously, is independent of Apaf-1 and cytochrome c. In the present work, we have used a set of complementary approaches, including two-dimensional gel electrophoresis coupled with matrix-assisted laser desorption ionization-time-of-flight mass spectrometry and nano-liquid chromatography-electrospray ionization mass spectrometry with tandem mass spectrometry, RNA interference, co-immunoprecipitation, immunodepletion of candidate proteins, and reconstitution studies, to identify mediators of the ER stress-induced cell death pathway. Our data identify two molecules, valosin-containing protein and apoptosis-linked gene-2 (ALG-2), that appear to play a role in mediating ER stress-induced cell death.
Collapse
Affiliation(s)
- Rammohan V Rao
- The Buck Institute for Age Research, Novato, California 94945, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Buckley KA, Golding SL, Rice JM, Dillon JP, Gallagher JA. Release and interconversion of P2 receptor agonists by human osteoblast-like cells. FASEB J 2003; 17:1401-10. [PMID: 12890693 DOI: 10.1096/fj.02-0940com] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Nucleotides, acting as agonists at P2 receptors, are important extracellular signaling molecules in many tissues. In bone they affect both bone-forming osteoblast and bone-resorbing osteoclast cell activity. The presence of nucleotides in the extracellular microenvironment is largely determined by their release from cells and metabolism by ecto-enzymes, both of which have scarcely been studied in bone. We have investigated adenosine 5'-triphosphate (ATP) release from SaOS-2 osteoblastic cells and the activities of cell surface ecto-enzymes on ATP metabolism. ATP, but not LDH, was detected in SaOS-2 cell conditioned medium, suggesting these cells were actively releasing ATP. Introduction of ADP resulted in increased ATP concentrations in the medium, which was found not to be receptor mediated. Nucleotide inhibition and substrate specificity studies revealed an ecto-nucleoside diphosphokinase (ecto-NDPK) was responsible for the ADP-->ATP conversion; PCR and immunocytochemistry confirmed its presence. Analysis of ATP metabolism over time demonstrated overall ATP degradation was increased by inhibiting ecto-NDPK activity; confirming that the combined action of multiple osteoblast-expressed ecto-enzymes affected extracellular nucleotide concentration. The data establish the coexistence of ATP-consuming, and for the first time, ATP-generating activities on the osteoblast cell surface, the discovery of which has significant implications for studies involving P2 receptor subtypes in bone.
Collapse
Affiliation(s)
- K A Buckley
- Human Bone Cell Research Group, Department of Human Anatomy and Cell Biology, University of Liverpool, L69 3GE, UK.
| | | | | | | | | |
Collapse
|
7
|
Com E, Evrard B, Roepstorff P, Aubry F, Pineau C. New insights into the rat spermatogonial proteome: identification of 156 additional proteins. Mol Cell Proteomics 2003; 2:248-61. [PMID: 12754304 DOI: 10.1074/mcp.m300010-mcp200] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Despite the essential role played by spermatogonia in testicular function, little is known about these cells. To improve our understanding of their biology, our group recently identified a set of 53 spermatogonial proteins using two-dimensional (2-D) gel electrophoresis and mass spectrometry. To continue this work, we investigated a subset of the spermatogonial proteome using narrow range immobilized pH gradients to favor the detection of less abundant proteins. A 2-D reference map of spermatogonia in the pH range 4-9 was created, and protein entities fractionated in a pH 5-6 2-D gel were further processed for protein identification. A new set of 156 polypeptides was identified by peptide mass fingerprinting and tandem mass spectrometry. These polypeptides corresponded to 102 different proteins, which reflect the complexity of post-translational modifications. Seventy-nine of these proteins were identified for the first time in spermatogonia. All identified proteins were classified into functional groups. This work represents a first step toward the establishment of a systematic spermatogonia protein database.
Collapse
Affiliation(s)
- Emmanuelle Com
- GERM-INSERM U.435, Campus de Beaulieu, Université de Rennes I, 35042 Rennes Cedex, Bretagne, France
| | | | | | | | | |
Collapse
|
8
|
Buxton IL, Kaiser RA, Oxhorn BC, Cheek DJ. Evidence supporting the Nucleotide Axis Hypothesis: ATP release and metabolism by coronary endothelium. Am J Physiol Heart Circ Physiol 2001; 281:H1657-66. [PMID: 11557556 DOI: 10.1152/ajpheart.2001.281.4.h1657] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The Nucleotide Axis Hypothesis, defined and supported herein, proposes that ATP stimulates the release of vasoactive mediators from endothelium, including ATP itself. Here, we show rapid endothelium-dependent, agonist-stimulated ATP elaboration in coronary vessels of guinea pigs. Measurement of extracellular ADP metabolism in intact vessels results in the time- and substrate-dependent formation of ATP in the coronary perfusate in amounts greater than can be accounted for by release from endothelium alone. ATP formation by endothelial cells is saturable (K(M) = 38.5 micromol/l, where K(M) is substrate concentration at which rate is half-maximal.) and trypsin-sensitive, membranes from [gamma-(32)P]ATP-labeled cells support ADP-dependent transphosphorylation by a 20-kDa protein, Western blots reveal the presence of a nucleoside diphosphate kinase (NDPK) of approximately 20 kDa in endothelial membranes, and analysis of NDPK antibody binding by flow cytometry is consistent with the presence of an ecto-NDPK on cardiac endothelial cells. Sequencing of the endothelial cell ecto-NDPK reveals a predicted amino acid sequence with 85% identity to human Nm23-H1 and consistent with a protein whose properties may confer membrane association as well as sites of regulation of activity. Our data underscore the potential importance of a nucleotide axis in cardiac blood vessels.
Collapse
Affiliation(s)
- I L Buxton
- Department of Pharmacology, University of Nevada School of Medicine, Reno, Nevada 89557, USA
| | | | | | | |
Collapse
|
9
|
Klinker JF, Seifert R. Nucleoside diphosphate kinase activity in soluble transducin preparations biochemical properties and possible role of transducin-beta as phosphorylated enzyme intermediate. EUROPEAN JOURNAL OF BIOCHEMISTRY 1999; 261:72-80. [PMID: 10103035 DOI: 10.1046/j.1432-1327.1999.00209.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Known nucleoside diphosphate kinases (NDPKs) are oligomers of 17-23-kDa subunits and catalyze the reaction N1TP + N2DP --> N1DP + N2TP via formation of a histidine-phosphorylated enzyme intermediate. NDPKs are involved in the activation of heterotrimeric GTP-binding proteins (G-proteins) by catalyzing the formation of GTP from GDP, but the properties of G-protein-associated NDPKs are still incompletely known. The aim of our present study was to characterize NDPK in soluble preparations of the retinal G-protein transducin. The NDPK is operationally referred to as transducin-NDPK. Like known NDPKs, transducin-NDPK utilizes NTPs and phosphorothioate analogs of NTPs as substrates. GDP was a more effective phosphoryl group acceptor at transducin-NDPK than ADP and CDP, and guanosine 5'-[gamma-thio]triphosphate (GTP[S]) was a more effective thiophosphoryl group donor than adenosine 5'-[gamma-thio]triphosphate (ATP[S]). In contrast with their action on known NDPKs, mastoparan and mastoparan 7 had no stimulatory effect on transducin-NDPK. Guanosine 5'-[beta, gamma-imido]triphosphate (p[NH]ppG) potentiated [3H]GTP[S] formation from [3H]GDP and ATP[S] but not [3H]GTP[S] formation from [3H]GDP and GTP[S]. Depending on the thiophosphoryl group acceptor and donor, [3H]NTP[S] formation was differentially regulated by Mg2+, Mn2+, Co2+, Ca2+ and Zn2+. [gamma-32P]ATP and [gamma-32P]GTP [32P]phosphorylated, and [35S]ATP[S] [35S]thiophosphorylated, a 36-kDa protein comigrating with transducin-beta. p[NH]ppG potentiated [35S]thiophosphorylation of the 36-kDa protein. 32P-labeling of the 36-kDa protein showed characteristics of histidine phosphorylation. There was no evidence for (thio)phosphorylation of 17-23-kDa proteins. Our data show the following: (a) soluble transducin preparations contain a GDP-prefering and guanine nucleotide-regulated NDPK; (b) transducin-beta may serve as a (thio)phosphorylated NDPK intermediate; (c) transducin-NDPK is distinct from known NDPKs and may consist of multiple kinases or a single kinase with multiple regulatory domains.
Collapse
Affiliation(s)
- J F Klinker
- Institut für Pharmakologie, Freie Universität Berlin, Germany
| | | |
Collapse
|
10
|
Ishijima Y, Shimada N, Fukuda M, Miyazaki H, Orlov NY, Orlova TG, Yamada T, Kimura N. Overexpression of nucleoside diphosphate kinases induces neurite outgrowth and their substitution to inactive forms leads to suppression of nerve growth factor- and dibutyryl cyclic AMP-induced effects in PC12D cells. FEBS Lett 1999; 445:155-9. [PMID: 10069391 DOI: 10.1016/s0014-5793(99)00116-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Whether nucleoside diphosphate kinase (NDPK) is involved in neuronal differentiation was investigated with special reference to its enzyme activity. Neurite outgrowth of PC12D cells induced by nerve growth factor or a cyclic AMP analog was suppressed to some extent when inactive NDPKs (the active site histidine 118 was replaced with alanine), not active forms, were transiently overexpressed. This suppression was more definite in their stably expressed clones. NDPKbeta-transfected clones and, to a lesser extent, NDPKalpha-transfected clones, but not inactive NDPK-transfected clones, extended neurites without differentiation inducers. These results imply that NDPKs may play a role by exerting their enzyme activity during differentiation of PC12 cells.
Collapse
Affiliation(s)
- Y Ishijima
- Department of Gene Regulation and Protein Function, Tokyo Metropolitan Institute of Gerontology, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Orlov NY, Orlova TG, Reshetnyak YK, Burstein EA, Kimura N. Comparative study of recombinant rat nucleoside diphosphate kinases alpha and beta by intrinsic protein fluorescence. J Biomol Struct Dyn 1999; 16:955-68. [PMID: 10217461 DOI: 10.1080/07391102.1999.10508304] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Nucleoside diphosphate (NDP) kinases of mammals are hexamers of two sorts of randomly associated highly homologous subunits of 152 residues each and, therefore exist in cell as NDP kinase isoforms. The catalytic properties and three-dimensional structures of the isoforms are very similar. The physiological meaning of the existence of the isoforms in cells remained unclear, but studying recombinant rat NDP kinases alpha and beta, each containing only one sort of subunits, we discovered that, in contrast to the isoenzyme beta, NDP kinase alpha is able to interact with the complex between bleached rhodopsin and G-protein transducin in retinal rod membranes at lowered pH values (Orlov et al. FEBS Lett. 389, 186-190, 1996). In order to search for possible molecular basis of such differences between these isoenzymes, a detailed comparative study of their intrinsic fluorescence properties in a large range of solvent conditions was performed in this work. The isoenzymes alpha and beta both contain the same three tryptophan (Trp78, 133, Ind 149) and four tyrosine (Tyr 52, 67, 147, and 151) residues per subunit, but exhibit pronounced differences in their fluorescence properties (both in spectral positions and shape and quantum yield values) and behave differently under pH titration. Whereas NDP kinase alpha undergoes spectral changes in the pH range 5-7 with the mid-point at 6.2, no unequivocal indication of a structural change of NDP kinase beta under pH titration from 9 to 5 was obtained. Since the pH dependencies obtained for fluorescence of isoenzyme alpha resembles the dependence of its binding to the rhodopsin-transducin complex it was suggested that the differences between the NDP kinase isoenzymes alpha and beta in the pH-induced behavior, revealed by the fluorescence spectroscopy, and the differences in their ability to interact with rhodopsin-transducin complex may have the same physical nature, that would be a physico-chemical reason of possible functional dissimilarity of NDP kinase isoforms in cell. An additional analysis of three-dimensional structure of homologous NDP kinases revealed that the source of the differences in fluorescence properties and pH-titration behavior between the isoenzymes alpha and beta may be due to the difference in their global electrostatic charges, rather than to any structural differences between them at neutral pH. The unusually high positive electrostatic potential at he deeply buried active site Tyr52 makes possible that it exists in deprotonated tyrosinate form at neutral and moderately acidic solution. Such a possibility may account for rather unusual fluorescence properties of NDP kinase alpha: (i) rather long-wavelength emission of NDP kinase alpha at ca. 340 nm at pH ca. 8 at extremely low accessibility to external quenchers and, possibly, (ii) an unusually high quantum yield value (ca. 0.42).
Collapse
Affiliation(s)
- N Y Orlov
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino.
| | | | | | | | | |
Collapse
|
12
|
Dabernat S, Larou M, Massé K, Hökfelt T, Mayer G, Daniel JY, Landry M. Cloning of a second nm23-M1 cDNA: expression in the central nervous system of adult mouse and comparison with nm23-M2 mRNA distribution. BRAIN RESEARCH. MOLECULAR BRAIN RESEARCH 1999; 63:351-65. [PMID: 9878823 DOI: 10.1016/s0169-328x(98)00300-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Nm23 has been identified as a gene family encoding different isoforms of the nucleoside diphosphate kinase. This protein is a key enzyme in the control of cellular concentrations of nucleoside triphosphates. Moreover, it has been shown to play important roles in various cellular functions such as differentiation and metastasis. In the present study, a second cDNA for nucleoside diphosphate kinase A (Nm23-M1) was isolated from a cDNA library of mouse embryonic stem cells. This clone encodes the same putative 152 aminoacids long protein as an already published cDNA but is longer in both its 5' and 3' untranslated regions. Tissue and cellular distribution of nm23-M1 mRNA was investigated by using Northern blot analysis and in situ hybridization. Nm23-M1 transcripts were found to be widely distributed throughout the mouse central nervous system with prominent expression in several restricted areas. No differences were noticed between the distribution of long and short transcripts. Furthermore, a similar pattern of expression was described in the central nervous system for nm23-M2 mRNA, encoding a second isoform of the nucleoside diphosphate kinase. However, the transcript of this isoform displayed a wider distribution and was expressed in all organs analysed by northern blotting. The possible involvement of nm23-M1 in differentiation of mouse nervous system is further discussed.
Collapse
Affiliation(s)
- S Dabernat
- Laboratoire de Biologie de la Différenciation et du Développement, Université Bordeaux 2, 146, rue Léo Saignat, 33 076, Bordeaux Cedex,
| | | | | | | | | | | | | |
Collapse
|
13
|
Otero AS. Copurification of vimentin, energy metabolism enzymes, and a MER5 homolog with nucleoside diphosphate kinase. Identification of tissue-specific interactions. J Biol Chem 1997; 272:14690-4. [PMID: 9169432 DOI: 10.1074/jbc.272.23.14690] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Chromatography on immobilized antibodies specific to nucleoside diphosphate (NDP) kinase was utilized for affinity purification of this enzyme from detergent extracts of frog heart post-mitochondrial fractions. SDS-polyacrylamide gel electrophoresis analysis of eluates from these supports shows that five polypeptides co-purify with nucleoside diphosphate (NDP) kinase. Tryptic digests of each band were analyzed by mass spectrometric microsequencing. Data base searches by peptide mass matching and sequence homology led to the identification of these proteins as glyceraldehyde-3-phosphate dehydrogenase (40 kDa), creatine kinase (45 kDa), vimentin (55 kDa), pyruvate kinase (60 kDa), and a putative member of the antioxidant protein family (28 kDa). Distinct protein compositions were found in eluates of lung and liver extracts processed in a like manner. The 28-kDa band and vimentin were associated with NDP kinase from all tissues, but co-purification of pyruvate kinase was seen only in liver, while creatine kinase and glyceraldehyde-3-phosphate dehydrogenase were absent from eluates from lung and liver. The results suggest that while NDP kinase is associated with vimentin intermediate filaments and an antioxidant protein in most tissues, it interacts with energy metabolism enzymes in a tissue-specific manner.
Collapse
Affiliation(s)
- A S Otero
- Department of Molecular Physiology and Biological Physics, University of Virginia Medical School, Charlottesville, Virginia 22906, USA.
| |
Collapse
|
14
|
Ishikawa N, Taniguchi-Seto H, Munakata Y, Takagi Y, Shimada N, Kimura N. Multiple transcripts for rat nucleoside diphosphate kinase alpha isoform are structurally categorized into two groups that exhibit cell-specific expression and distinct translation potential. J Biol Chem 1997; 272:3289-95. [PMID: 9013567 DOI: 10.1074/jbc.272.6.3289] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Rat nucleoside diphosphate (NDP) kinase is composed of two isoforms (alpha and beta) encoded by independent genes. The mRNAs are expressed ubiquitously; however, the level of expression is tissue-dependent and is also up- or down-regulated under certain conditions, including growth stimulation, differentiation, and tumor metastasis. To address the regulatory mechanisms of gene expression for the rat NDP kinase major isoform alpha (an nm23-H2/PuF homologue), we identified the transcription initiation sites in detail by RNase protection and 5'-rapid amplification of DNA ends and located the core promoter region by chloramphenicol acetyltransferase assay. The transcripts, initiated from an extraordinarily wide range of sites, were categorized into two groups; one transcribed from an upstream region was spliced in the untranslated region (group 1), whereas the other initiated in the downstream region was not (group 2). RNase protection demonstrated that the group 1 mRNA was the dominant form present in all tissues except heart and skeletal muscle. In situ hybridization revealed cell-specific expression of these mRNA species. Furthermore, they differed in the translational efficiency (the group 2 alpha > beta > the group 1 alpha). These findings suggest that the regulation of the NDP kinase expression at both transcriptional and posttranscriptional steps could be fundamentally governed by the selection of transcription initiation sites.
Collapse
Affiliation(s)
- N Ishikawa
- Department of Molecular Pathology, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakaecho, Itabashi-ku, Tokyo 173, Japan.
| | | | | | | | | | | |
Collapse
|
15
|
Orlov NY, Orlova TG, Nomura K, Hanai N, Kimura N. Transducin-mediated, isoform-specific interaction of recombinant rat nucleoside diphosphate kinases with bleached bovine retinal rod outer segment membranes. FEBS Lett 1996; 389:186-90. [PMID: 8766826 DOI: 10.1016/0014-5793(96)00575-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The properties of the binding of recombinant rat nucleoside diphosphate (NDP) kinase isoforms alpha and beta (NDP kinase alpha and beta, respectively) to bleached bovine retinal rod outer segment (ROS) membranes were investigated. It was found that: (1) both NDP kinase isoforms interacted with ROS membranes in a pH-, cation- and GTPgammaS-dependent manner; (2) the retinal G-protein transducin was an obligatory factor for the interaction; (3) the apparent affinity of NDP kinase alpha for ROS membranes was about 100-fold higher than that of NDP kinase beta; and (4) an alpha-isoform-specific peptide, corresponding to the sequence of the N-terminal third (variable region), had the ability to displace bovine NDP kinase from ROS membranes. The results suggest the possible involvement of NDP kinases in cellular regulation via interaction with G-proteins and provide a structural basis for the possible differential roles of mammalian NDP kinase isoforms in the cell.
Collapse
Affiliation(s)
- N Y Orlov
- Department of Molecular Biology, Tokyo Metropolitan Institute of Gerontology, Japan
| | | | | | | | | |
Collapse
|
16
|
Yi XB, Seitzer NM, de S Otero A. Neutralizing antibodies to nucleoside diphosphate kinase inhibit the enzyme in vitro and in vivo: evidence for two distinct mechanisms of activation of atrial currents by ATPgammaS. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1310:334-42. [PMID: 8599612 DOI: 10.1016/0167-4889(95)00164-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Nucleoside diphosphate kinase (NDPK) participates in multiple cellular functions, yet the molecular mechanisms of its involvement are often unknown, given that there are no specific inhibitors for the enzyme from vertebrates. We developed antibodies against NDPK by immunization of rabbits with the enzyme from bullfrog skeletal muscle. The antibodies specifically recognized the enzyme from frog tissues, and cross-reacted with NDPK from Xenopus. In contrast to mammalian NDPK, the amphibian enzyme elicited antibodies that inhibit potently its catalytic function. We utilized the inhibitory properties of these immunoglobulins to examine the role of NDPK on the ATPgammaS-induced stimulation of Ca2+ and K+ currents of cardiac myocytes. Injection of NDPK-neutralizing Fab fragments into atrial cells reduced considerably the effect of ATPgammaS on muscarinic K+ currents, but not on Ca2+ currents. Therefore, ATPgammaS increases calcium and potassium currents of atrial cells by two distinct mechanisms. NDPK is essential for the conversion of ATPgammaS into GTPgammaS which leads to muscarinic K+ channel activation but not for the stimulation of Ca2+ currents by ATPgammaS. The results demonstrate that antibodies to frog NDPK block the activity of the enzyme in vivo and in vitro, and can be used to determine the relevance of NDPK and its catalytic activity to the function of vertebrate cells.
Collapse
Affiliation(s)
- X B Yi
- Department of Molecular Physiology and Biological Physics, University of Virginia Medical School, Charlottesville, 22908, USA
| | | | | |
Collapse
|
17
|
Klinker JF, Laugwitz KL, Hagelüken A, Seifert R. Activation of GTP formation and high-affinity GTP hydrolysis by mastoparan in various cell membranes. G-protein activation via nucleoside diphosphate kinase, a possible general mechanism of mastoparan action. Biochem Pharmacol 1996; 51:217-23. [PMID: 8573186 DOI: 10.1016/0006-2952(95)02119-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The wasp venom, mastoparan (MP), is a direct activator of reconstituted pertussis toxin-sensitive G-proteins and of purified nucleoside diphosphate kinase (NDPK) [E.C. 2.6.4.6.]. In HL-60 membranes, MP activates high-affinity GTPase [E.C. 3.6.1.-] and NDPK-catalyzed GTP formation, but not photolabeling of G-protein alpha-subunits with GTP azidoanilide; this suggests that the venom activates G-proteins in this system indirectly via stimulation of NDPK. Moreover, the MP analogue, mastoparan 7 (MP 7), is a much more effective activator of reconstituted G-proteins than MP, whereas with regard to NDPK and GTPase in HL-60 membranes, the two peptides are similarly effective. In our present study, we investigated NDPK- and G-protein activation by MP in membranes of the human neuroblastoma cell line, SH-SY5Y, the human erythroleukemia cell line, HEL, the rat basophilic leukemia cell line, RBL 2H3, and the hamster ductus deferens smooth muscle cell line, DDT1MF-2. All these membranes exhibited high NDPK activities that were increased by MP. Compared to basal GTP formation rates, basal rates of high-affinity GTP hydrolysis in cell membranes were low. MP activated high-affinity GTP hydrolysis in cell membranes but did not enhance incorporation of GTP azidoanilide into G-protein alpha-subunits. As with HL-60 membranes, MP and MP 7 were similarly effective activators of NDPK and GTPase in SH-SY5Y membranes. Pertussis toxin inhibited MP-stimulated GTP hydrolyses in SH-SY5Y- and HEL membranes, whereas NDPK activations by MP were pertussis toxin-insensitive. Our data suggest that indirect G-protein activation via NDPK is not restricted to HL-60 membranes but is a more general mechanism of MP action in cell membranes. Pertussis toxin-catalyzed ADP-ribosylation of alpha-subunits may inhibit the transfer of GTP from NDPK to G-proteins. NDPK may play a much more important role in transmembrane signal transduction than was previously appreciated and, moreover, the GTPase of G-protein alpha-subunits may serve as GDP-synthase for NDPK.
Collapse
Affiliation(s)
- J F Klinker
- Institut für Pharmakologie, Freie Universitat Berlin, Germany
| | | | | | | |
Collapse
|
18
|
Fukuda M, Ishii A, Yasutomo Y, Shimada N, Ishikawa N, Hanai N, Nagata N, Irimura T, Nicolson GL, Kimura N. Decreased expression of nucleoside diphosphate kinase alpha isoform, an nm23-H2 gene homolog, is associated with metastatic potential of rat mammary-adenocarcinoma cells. Int J Cancer 1996; 65:531-7. [PMID: 8621239 DOI: 10.1002/(sici)1097-0215(19960208)65:4<531::aid-ijc23>3.0.co;2-b] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The nm23 gene [encoding nucleoside diphosphate kinase (NDPK)] may act as a metastasis suppressor in certain tumor cells. We investigated the role of NDPK isoforms (alpha and beta) in the metastatic processes, using rat mammary-adenocarcinoma cell lines of poor (MTC) and high (MTLn3) spontaneous metastatic potential respectively. In these cell lines, as in most rat tissues, the alpha isoform (nm23-H2 homolog) was more highly expressed than the beta isoform (nm23-H1 homolog) at the mRNA and protein levels. When examined by Northern- and Western-blot analyses, expression of the 2 isoforms was reduced in highly metastatic MTLn3 cells compared with poorly metastatic MTC cells. The reduced expression was also associated with diminished NDPK-enzyme activity in the cell extracts. Southern-blot and RT-PCR-SSCP analyses suggested that the 2 genes were not grossly altered or mutated in their translation regions. MTLn3 cell clones transfected with NDPKalpha or NDPKbeta cDNA were all tumorigenic when implanted into the mammary fat pad of syngeneic rats. Among those, only clones transfected with the NDPKalpha gene exhibited reduced lung metastasis in a spontaneous metastasis assay.
Collapse
Affiliation(s)
- M Fukuda
- Department of Molecular Biology, Tokyo Metropolitan Institute of Gerontology, Japan
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Ohneda K, Fukuda M, Shimada N, Ishikawa N, Ichou T, Kaji K, Toyota T, Kimura N. Increased expression of nucleoside diphosphate kinases/nm23 in human diploid fibroblasts transformed by SV40 large T antigen or 60Co irradiation. FEBS Lett 1994; 348:273-7. [PMID: 8034053 DOI: 10.1016/0014-5793(94)00623-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
When the expression levels of nucleoside diphosphate (NDP) kinase/nm23 were examined in four human normal diploid fibroblast cell lines in comparison with their corresponding immortalized cells transformed by SV40 large T antigen or 60Co irradiation, mRNA levels of the two isoforms (NDP kinase A/nm23-H1, NDP kinase B/nm23-H2) were increased in the immortalized cell lines. The increase was found to be associated with increased translation products. Furthermore, the cell extracts prepared from these immortalized cell lines demonstrated slightly higher enzyme activity than those from their normal counterparts. Neither the growth state nor the in vitro aging largely affected their expression in a normal cell line (TIG-3) examined. The results suggest possible involvement of NDP kinases/nm23 in acquiring an infinite growth property of these cells.
Collapse
Affiliation(s)
- K Ohneda
- Department of Molecular Biology, Tokyo Metropolitan Institute of Gerontology, Japan
| | | | | | | | | | | | | | | |
Collapse
|