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Abstract
The NME (Non-metastatic) family members, also known as NDPKs (nucleoside diphosphate kinases), were originally identified and studied for their nucleoside diphosphate kinase activities. This family of kinases is extremely well conserved through evolution, being found in prokaryotes and eukaryotes, but also diverges enough to create a range of complexity, with homologous members having distinct functions in cells. In addition to nucleoside diphosphate kinase activity, some family members are reported to possess protein-histidine kinase activity, which, because of the lability of phosphohistidine, has been difficult to study due to the experimental challenges and lack of molecular tools. However, over the past few years, new methods to investigate this unstable modification and histidine kinase activity have been reported and scientific interest in this area is growing rapidly. This review presents a global overview of our current knowledge of the NME family and histidine phosphorylation, highlighting the underappreciated protein-histidine kinase activity of NME family members, specifically in human cells. In parallel, information about the structural and functional aspects of the NME family, and the knowns and unknowns of histidine kinase involvement in cell signaling are summarized.
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Affiliation(s)
| | | | | | - Tony Hunter
- Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; (K.A.); (J.N.); (J.R.)
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2
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Radić M, Šoštar M, Weber I, Ćetković H, Slade N, Herak Bosnar M. The Subcellular Localization and Oligomerization Preferences of NME1/NME2 upon Radiation-Induced DNA Damage. Int J Mol Sci 2020; 21:ijms21072363. [PMID: 32235358 PMCID: PMC7177722 DOI: 10.3390/ijms21072363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/20/2020] [Accepted: 03/26/2020] [Indexed: 02/06/2023] Open
Abstract
Nucleoside diphosphate kinases (NDPK/NME/Nm23) are enzymes composed of subunits NME1/NDPK A and NME2/NDPK B, responsible for the maintenance of the cellular (d)NTP pool and involved in other cellular processes, such as metastasis suppression and DNA damage repair. Although eukaryotic NDPKs are active only as hexamers, it is unclear whether other NME functions require the hexameric form, and how the isoenzyme composition varies in different cellular compartments. To examine the effect of DNA damage on intracellular localization of NME1 and NME2 and the composition of NME oligomers in the nucleus and the cytoplasm, we used live-cell imaging and the FRET/FLIM technique. We showed that exogenous NME1 and NME2 proteins co-localize in the cytoplasm of non-irradiated cells, and move simultaneously to the nucleus after gamma irradiation. The FRET/FLIM experiments imply that, after DNA damage, there is a slight shift in the homomer/heteromer balance between the nucleus and the cytoplasm. Collectively, our results indicate that, after irradiation, NME1 and NME2 engage in mutual functions in the nucleus, possibly performing specific functions in their homomeric states. Finally, we demonstrated that fluorophores fused to the N-termini of NME polypeptides produce the largest FRET effect and thus recommend this orientation for use in similar studies.
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Affiliation(s)
- Martina Radić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.R.); (N.S.)
| | - Marko Šoštar
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.Š.); (I.W.); (H.Ć.)
| | - Igor Weber
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.Š.); (I.W.); (H.Ć.)
| | - Helena Ćetković
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.Š.); (I.W.); (H.Ć.)
| | - Neda Slade
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.R.); (N.S.)
| | - Maja Herak Bosnar
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (M.R.); (N.S.)
- Correspondence: ; Tel.: +385-1-456-0996
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3
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Sengupta P, Bhattacharya A, Sa G, Das T, Chatterjee S. Truncated G-Quadruplex Isomers Cross-Talk with the Transcription Factors To Maintain Homeostatic Equilibria in c-MYC Transcription. Biochemistry 2019; 58:1975-1991. [PMID: 30920805 DOI: 10.1021/acs.biochem.9b00030] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The nuclease hypersensitive element III1 (NHE III1) upstream c-MYC promoter harbors a transcription-silencing G-quadruplex (Pu27) element. Dynamic turnover of various transcription factors (TFs) across Pu27 to control c-MYC transcription homeostasis is enigmatic. Here, we reveal that native Pu27 evolves truncated G-quadruplex isomers (Pu19, Pu22, Pu24, and Pu25) in cells that are optimal intracellular targets of specific TFs in a sequence- and structure-dependent manner. Nuclear magnetic resonance and isothermal titration calorimetry envisaged that NM23-H2 (nucleoside diphosphate kinase) and nucleolin induce conformational fluctuations in Pu27 to sample specific conformationally restricted conformer(s). Structural investigations revealed that the flanking guanines at 5'-Pu27 control solvent exposure at G-quartets upon NM23-H2 and nucleolin binding driving Pu27 unfolding and folding, respectively. Transient chromatin immunoprecipitations confirmed that NM23-H2 drives the conformation switch to Pu24 that outcompetes nucleolin recruitment. Similarly, nucleolin arrests Pu27 in the Pu22 conformer minimizing NM23-H2 binding at Pu27. hnRNPK (heterogeneous nuclear ribonucleoprotein K) positively regulates NM23-H2 and nucleolin association at Pu27 despite their antagonism. On the basis of these results, we simulated the transcription kinetics in a feed-forward loop in which the transcription output responds to hnRNPK-induced early activation via NM23-H2 association, which favors Pu24 formation at NHE III1 reducing nucleolin occupancy and driving quadruplex unfolding to initiate transcription. NM23-H2 further promotes hnRNPK deposition across NHE III1 altering Pu27 plasticity that finally enriches the nucleolin abundance to drive Pu22 formation and weaken NM23-H2 binding to extinguish transcription. This mechanism involves three positive feedback loops (NM23-H2-hnRNPK, NM23-H2-CNBP, and hnRNPK-nucleolin) and one negative feedback loop (NM23-H2-nucleolin) controlling optimal turnover and residence time of TFs at Pu27 to homeostatically regulate c-MYC transcription.
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Affiliation(s)
- Pallabi Sengupta
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Apoorva Bhattacharya
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Gaurisankar Sa
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Tanya Das
- Division of Molecular Medicine , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
| | - Subhrangsu Chatterjee
- Department of Biophysics , Bose Institute , P 1/12, C. I. T. Road, Scheme-VIIM , Kolkata 700054 , West Bengal , India
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Xu D, Aka JA, Wang R, Lin SX. 17beta-hydroxysteroid dehydrogenase type 5 is negatively correlated to apoptosis inhibitor GRP78 and tumor-secreted protein PGK1, and modulates breast cancer cell viability and proliferation. J Steroid Biochem Mol Biol 2017; 171:270-280. [PMID: 28457968 DOI: 10.1016/j.jsbmb.2017.04.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Revised: 04/15/2017] [Accepted: 04/19/2017] [Indexed: 01/14/2023]
Abstract
17beta-hydroxysteroid dehydrogenase type 5 (17β-HSD5) is an important enzyme associated with sex steroid metabolism in hormone-dependent cancer. However, reports on its expression and its prognostic value in breast cancer are inconsistent. Here, we demonstrate the impact of 17β-HSD5 expression modulation on the proteome of estrogen receptor-positive (ER+) breast cancer cells. RNA interference technique (siRNA) was used to knock down 17β-HSD5 gene expression in the ER+ breast cancer cell line MCF-7 and the proteome of the 17β-HSD5-knockdown cells was compared to that of MCF-7 cells using two-dimensional (2-D) gel electrophoresis followed by mass spectrometry analysis. Ingenuity pathway analysis (IPA) was additionally used to assess functional enrichment analyses of the proteomic dataset, including protein network and canonical pathways. Our proteomic analysis revealed only four differentially expressed protein spots (fold change > 2, p<0.05) between the two cell lines. The four spots were up-regulated in 17β-HSD5-knockdown MCF-7 cells, and comprised 21 proteins involved in two networks and in functions that include apoptosis inhibition, regulation of cell growth and differentiation, signal transduction and tumor metastasis. Among the proteins are nucleoside diphosphate kinase A (NME1), 78kDa glucose-regulated protein (GRP78) and phosphoglycerate kinase 1 (PGK1). We also showed that expression of 17β-HSD5 and that of the apoptosis inhibitor GRP78 are strongly but negatively correlated. Consistent with their opposite regulation, GRP78 knockdown decreased MCF-7 cell viability whereas 17β-HSD5 knockdown or inhibition increased cell viability and proliferation. Besides, IPA analysis revealed that ubiquitination pathway is significantly affected by 17β-HSD5 knockdown. Furthermore, IPA predicted the proto-oncogene c-Myc as an upstream regulator linked to the tumor-secreted protein PGK1. The latter is over-expressed in invasive ductal breast carcinoma as compared with normal breast tissue and its expression increased following 17β-HSD5 knockdown. Our present results indicate a 17β-HSD5 role in down-regulating breast cancer development. We thus propose that 17β-HSD5 may not be a potent target for breast cancer treatment but its low expression could represent a poor prognosis factor.
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Affiliation(s)
- Dan Xu
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Laval University, 2705 Boulevard Laurier, Quebec City, Québec G1V 4G2, Canada
| | - Juliette A Aka
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Laval University, 2705 Boulevard Laurier, Quebec City, Québec G1V 4G2, Canada
| | - Ruixuan Wang
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Laval University, 2705 Boulevard Laurier, Quebec City, Québec G1V 4G2, Canada
| | - Sheng-Xiang Lin
- Laboratory of Molecular Endocrinology and Oncology, Centre Hospitalier Universitaire de Québec Research Centre (CHUQ, CHUL) and Department of Molecular Medicine, Laval University, 2705 Boulevard Laurier, Quebec City, Québec G1V 4G2, Canada.
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5
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You DJ, Park CR, Mander S, Ahn C, Seong JY, Hwang JI. Characterization of Functional Domains in NME1L Regulation of NF-κB Signaling. Mol Cells 2016; 39:403-9. [PMID: 27094059 PMCID: PMC4870188 DOI: 10.14348/molcells.2016.2320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/24/2016] [Accepted: 02/29/2016] [Indexed: 11/27/2022] Open
Abstract
NME1 is a well-known metastasis suppressor which has been reported to be downregulated in some highly aggressive cancer cells. Although most studies have focused on NME1, the NME1 gene also encodes the protein (NME1L) containing N-terminal 25 extra amino acids by alternative splicing. According to previous studies, NME1L has potent anti-metastatic activity, in comparison with NME1, by interacting with IKKβ and regulating its activity. In the present study, we tried to define the role of the N-terminal 25 amino acids of NME1L in NF-κB activation signaling. Unfortunately, the sequence itself did not interact with IKKβ, suggesting that it may be not enough to constitute the functional structure. Further construction of NME1L fragments and biochemical analysis revealed that N-terminal 84 residues constitute minimal structure for homodimerization, IKKβ interaction and regulation of NF-κB signaling. The inhibitory effect of the fragment on cancer cell migration and NF-κB-stimulated gene expression was equivalent to that of whole NME1L. The data suggest that the N-terminal 84 residues may be a core region for the anti-metastatic activity of NME1L. Based on this result, further structural analysis of the binding between NME1L and IKKβ may help in understanding the anti-metastatic activity of NME1L and provide direction to NME1L and IKKβ-related anti-cancer drug design.
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Affiliation(s)
- Dong-Joo You
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Cho Rong Park
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Sunam Mander
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Curie Ahn
- Transplantation Research Institute, Cancer Research Institute, Seoul National University, Seoul 110-799,
Korea
| | - Jae Young Seong
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
| | - Jong-Ik Hwang
- Graduate School of Medicine, Korea University, Seoul 136-705,
Korea
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Smagghe BJ, Stewart AK, Carter MG, Shelton LM, Bernier KJ, Hartman EJ, Calhoun AK, Hatziioannou VM, Lillacci G, Kirk BA, DiNardo BA, Kosik KS, Bamdad C. MUC1* ligand, NM23-H1, is a novel growth factor that maintains human stem cells in a more naïve state. PLoS One 2013; 8:e58601. [PMID: 23505541 PMCID: PMC3591366 DOI: 10.1371/journal.pone.0058601] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 02/07/2013] [Indexed: 12/20/2022] Open
Abstract
We report that a single growth factor, NM23-H1, enables serial passaging of both human ES and iPS cells in the absence of feeder cells, their conditioned media or bFGF in a fully defined xeno-free media on a novel defined, xeno-free surface. Stem cells cultured in this system show a gene expression pattern indicative of a more “naïve” state than stem cells grown in bFGF-based media. NM23-H1 and MUC1* growth factor receptor cooperate to control stem cell self-replication. By manipulating the multimerization state of NM23-H1, we override the stem cell's inherent programming that turns off pluripotency and trick the cells into continuously replicating as pluripotent stem cells. Dimeric NM23-H1 binds to and dimerizes the extra cellular domain of the MUC1* transmembrane receptor which stimulates growth and promotes pluripotency. Inhibition of the NM23-H1/MUC1* interaction accelerates differentiation and causes a spike in miR-145 expression which signals a cell's exit from pluripotency.
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Affiliation(s)
- Benoit J. Smagghe
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Andrew K. Stewart
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Mark G. Carter
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Laura M. Shelton
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Kyle J. Bernier
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Eric J. Hartman
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Amy K. Calhoun
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | | | - Gabriele Lillacci
- Department of Mechanical Engineering, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Brian A. Kirk
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Brian A. DiNardo
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
| | - Kenneth S. Kosik
- The Neuroscience Research Institute and the Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America
| | - Cynthia Bamdad
- Minerva Biotechnologies, Waltham, Massachusetts, United States of America
- * E-mail:
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Quintero-Reyes IE, Garcia-Orozco KD, Sugich-Miranda R, Arvizu-Flores AA, Velazquez-Contreras EF, Castillo-Yañez FJ, Sotelo-Mundo RR. Shrimp oncoprotein nm23 is a functional nucleoside diphosphate kinase. J Bioenerg Biomembr 2012; 44:325-31. [PMID: 22528393 DOI: 10.1007/s10863-012-9436-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 03/19/2012] [Indexed: 11/27/2022]
Abstract
Biosynthesis of nucleoside triphosphates is critical for bioenergetics and nucleic acid replication, and this is achieved by nucleoside diphosphate kinase (NDK). As an emerging biological model and the global importance of shrimp culture, we have addressed the study of the Pacific whiteleg shrimp (Litopenaeus vannamei) NDK. We demonstrated its activity and affinity towards deoxynucleoside diphosphates. Also, the quaternary structure obtained by gel filtration chromatography showed that shrimp NDK is a trimer. Affinity was in the micro-molar range for dADP, dGDP, dTDP and except for dCDP, which presented no detectable interaction by isothermal titration calorimetry, as described previously for Plasmodium falciparum NDK. This information is particularly important, as this enzyme could be used to test nucleotide analogs that can block white spot syndrome virus (WSSV) viral replication and to study its bioenergetics role during hypoxia and fasting.
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Affiliation(s)
- Idania E Quintero-Reyes
- Aquatic Molecular Biology Lab, Centro de Investigación en Alimentación y Desarrollo A.C., Carretera a Ejido la Victoria Km 0.6, Hermosillo, Sonora 83304, Mexico
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Perina D, Bosnar MH, Mikoč A, Müller WEG, Cetković H. Characterization of Nme6-like gene/protein from marine sponge Suberites domuncula. Naunyn Schmiedebergs Arch Pharmacol 2011; 384:451-60. [PMID: 21533994 DOI: 10.1007/s00210-011-0635-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/05/2011] [Indexed: 11/26/2022]
Abstract
Nucleoside diphosphate kinases (NDPKs) are evolutionarily conserved enzymes involved in many biological processes such as metastasis, proliferation, development, differentiation, ciliary functions, vesicle transport and apoptosis in vertebrates. Biochemical mechanisms of these processes are still largely unknown. Sponges (Porifera) are simple metazoans without tissues, closest to the common ancestor of all animals. They changed little during evolution and probably provide the best insight into the metazoan ancestors' genomic features. The purpose of this study was to address structural and functional properties of group II Nme6 gene/protein ortholog from the marine sponge Suberites domuncula, Nme6, in order to elucidate its evolutionary history. Sponge Nme6 gene and promoter were sequenced and analysed with various bioinformatical tools. Nme6 and Nme6Δ31 proteins were produced in E. coli strain BL21 and NDPK activity was measured using a coupled pyruvate kinase-lactate dehydrogenase assay. Subcellular localization in human tumour cells was examined by confocal scanning microscopy. Our results show that the sponge Nme6 compared to human Nme6 does not possess NDPK activity, does not localize in mitochondria at least in human cells although it has a putative mitochondrial signal sequence, lacks two recent introns that comprise miRNAs and have different transcriptional binding sites in the promoter region. Therefore, we conclude that the structure of Nme6 gene has changed during metazoan evolution possibly in correlation with the function of the protein.
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Affiliation(s)
- Drago Perina
- Laboratory of Molecular Genetics, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, P.P. 180, 10002, Zagreb, Croatia
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9
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Abstract
The metastasis suppressor NM23-H1 possesses 3 enzymatic activities in vitro, a nucleoside diphosphate kinase (NDPK), a protein histidine kinase and a more recently characterized 3'-5' exonuclease. Although the histidine kinase has been implicated in suppression of motility in breast carcinoma cell lines, potential relevance of the NDPK and 3'-5' exonuclease to metastasis suppressor function has not been addressed in detail. To this end, site-directed mutagenesis and biochemical analyses of bacterially expressed mutant NM23-H1 proteins have identified mutations that disrupt the 3'-5' exonuclease alone (Glu(5) to Ala, or E(5) A), the NDPK and histidine kinase activities tandemly (Y(52) A, H(118) F) or all 3 activities simultaneously (K(12) Q). Although forced expression of NM23-H1 potently suppressed spontaneous lung metastasis of subcutaneous tumor explants derived from the human melanoma cell line 1205LU, no significant metastasis suppressor activity was obtained with the exonuclease-deficient variants E(5) A and K(12) Q. The H(118) F mutant, which lacked both the NDPK and histidine kinase while retaining the 3'-5' exonuclease, also exhibited compromised suppressor activity. In contrast, each mutant retained the ability to suppress motility and invasive characteristics of 1205LU cells in culture, indicating that the NM23-H1 molecule possesses an additional activity(s) mediating these suppressor functions. These studies provide the first demonstration that the 3'-5' exonuclease activity of NM23-H1 is necessary for metastasis suppressor function and further indicate cooperativity of the 3 enzymatic activities of the molecule on suppression of the metastatic process.
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MESH Headings
- Amino Acid Sequence
- Animals
- Blotting, Western
- Cell Line, Tumor
- Cell Movement
- Cell Proliferation
- Exonucleases/chemistry
- Exonucleases/genetics
- Exonucleases/metabolism
- Female
- Glutamic Acid/genetics
- Glutamic Acid/metabolism
- Histidine/genetics
- Histidine/metabolism
- Histidine Kinase
- Humans
- Lung Neoplasms/enzymology
- Lung Neoplasms/genetics
- Lung Neoplasms/secondary
- Lysine/genetics
- Lysine/metabolism
- Melanoma, Experimental/enzymology
- Melanoma, Experimental/genetics
- Melanoma, Experimental/pathology
- Mice
- Mice, Nude
- Models, Molecular
- Molecular Sequence Data
- Mutagenesis, Site-Directed
- Mutation, Missense
- NM23 Nucleoside Diphosphate Kinases/chemistry
- NM23 Nucleoside Diphosphate Kinases/genetics
- NM23 Nucleoside Diphosphate Kinases/metabolism
- Protein Conformation
- Protein Kinases/chemistry
- Protein Kinases/genetics
- Protein Kinases/metabolism
- Reverse Transcriptase Polymerase Chain Reaction
- Transplantation, Heterologous
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Affiliation(s)
- Qingbei Zhang
- Department of Molecular and Biomedical Pharmacology, University of Kentucky College of Medicine, Lexington, KY 40536-0298, USA
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10
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Abstract
BACKGROUND The Nme family, previously known as Nm23 or NDPK, is involved in various molecular processes including tumor metastasis and some members of the family, but not all, exhibit a Nucleoside Diphosphate Kinase (NDPK) activity. Ten genes are known in humans, in which some members have been extensively studied. In non-mammalian species, the Nme protein family has received, in contrast, far less attention. The picture of the vertebrate Nme family remains thus incomplete and orthology relationships with mammalian counterparts were only partially characterized. The present study therefore aimed at characterizing the Nme gene repertoire in vertebrates with special interest for teleosts, and providing a comprehensive overview of the Nme gene family evolutionary history in vertebrates. RESULTS In the present study, we present the evolutionary history of the Nme family in vertebrates and characterize the gene family repertoire for the first time in several non-mammalian species. Our observations show that vertebrate Nme genes can be separated in two evolutionary distinct groups. Nme1, Nme2, Nme3, and Nme4 belong to Group I while vertebrate Nme5, Nme6, Nme7, Nme8, and Nme9 belong to Group II. The position of Nme10 is in contrast more debatable due to its very specific evolutionary history. The present study clearly indicates that Nme5, Nme6, Nme7, and Nme8 originate from duplication events that occurred before the chordate radiation. In contrast, Nme genes of the Group I have a very different evolutionary history as our results suggest that they all arise from a common gene present in the chordate ancestor. In addition, expression patterns of all zebrafish nme transcripts were studied in a broad range of tissues by quantitative PCR and discussed in the light of the function of their mammalian counterparts. CONCLUSION This work offers an evolutionary framework that will pave the way for future studies on vertebrate Nme proteins and provides a unified vertebrate Nme nomenclature that is consistent with the nomenclature in use in mammals. Based on protein structure and expression data, we also provide new insight into molecular functions of Nme proteins among vertebrates and raise intriguing questions on the roles of Nme proteins in gonads.
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Affiliation(s)
- Thomas Desvignes
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France
- IFREMER, LALR, F-34250 Palavas Les Flots, France
| | - Pierre Pontarotti
- UMR 6632/IFR48 Université de Aix Marseille/CNRS. Equipe Evolution biologique et Modélisation, case 19, 3 place Victor Hugo, 13331 Marseille Cedex 03, France
| | | | - Julien Bobe
- INRA, UR1037 SCRIBE, IFR140, Ouest-Genopole, F-35000 Rennes, France
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11
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Tokarska-Schlattner M, Boissan M, Munier A, Borot C, Mailleau C, Speer O, Schlattner U, Lacombe ML. The nucleoside diphosphate kinase D (NM23-H4) binds the inner mitochondrial membrane with high affinity to cardiolipin and couples nucleotide transfer with respiration. J Biol Chem 2008. [PMID: 18635542 DOI: 10.74/jbc.m803132200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
Nucleoside diphosphate kinase (NDPK/Nm23), responsible for intracellular di- and triphosphonucleoside homeostasis, plays multiple roles in cellular energetics, signaling, proliferation, differentiation and tumor invasion. The only human NDPK with a mitochondrial targeting sequence is NDPK-D, the NME4 gene product, which is a peripheral protein of mitochondrial membranes. Subfractionation of rat liver and HEK 293 cell mitochondria revealed that NDPK-D is essentially bound to the inner membrane. Surface plasmon resonance analysis of the interaction using recombinant NDPK-D and model liposomes showed that NDPK-D interacts electrostatically with anionic phospholipids, with highest affinity observed for cardiolipin. Mutation of the central arginine (Arg-90) in a surface-exposed basic RRK motif unique to NDPK-D strongly reduced interaction with anionic phospholipids. Due to its symmetrical hexameric structure, NDPK-D was able to cross-link anionic phospholipid-containing liposomes, suggesting that NDPK-D could promote intermembrane contacts. Latency assays with isolated mitochondria and antibody binding to mitoplasts indicated a dual orientation for NDPK-D. In HeLa cells, stable expression of wild type but not of the R90D mutant led to membrane-bound enzyme in vivo. Respiration was significantly stimulated by the NDPK substrate TDP in mitochondria containing wild-type NDPK-D, but not in those expressing the R90D mutant, which is catalytically equally active. This indicates local ADP regeneration in the mitochondrial intermembrane space and a tight functional coupling of NDPK-D with oxidative phosphorylation that depends on its membrane-bound state.
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12
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Napolitano F, D'Angelo F, Bimonte M, Perrina V, D'Ambrosio C, Scaloni A, Russo T, Zambrano N. A differential proteomic approach reveals an evolutionary conserved regulation of Nme proteins by Fe65 in C. elegans and mouse. Neurochem Res 2008; 33:2547-55. [PMID: 18401706 DOI: 10.1007/s11064-008-9683-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2007] [Accepted: 03/18/2008] [Indexed: 11/24/2022]
Abstract
The function of the APP-Fe65 complex is still not definitively understood. To address this point we studied the phenotype of Fe65 (feh-1) ablation, which results in severe developmental defects in C. elegans, including embryonic and larval arrests. To shed light on the complex phenotype of embryonic arrest, we undertook a systematic approach, aiming at the definition of the altered proteomic profile of feh-1 null worms. We defined a panel of 27 regulated proteins, 16 of which actually participating to embryonic development processes in the nematode. Protein spots corresponding to the products of the F25H2.5 gene, the nematode orthologue of mammalian Nm23/Nme gene family members, were consistently up-regulated in feh-1 -/- embryos. We observed similar up-regulation of Nme1 and Nme2 genes, both at the transcript and the protein levels, in the brain of Fe65 knock-out mice, thus highlighting the occurrence of evolutionary conserved mechanisms of Nme expression in nematodes and mammals.
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Affiliation(s)
- Francesco Napolitano
- CEINGE Biotecnologie Avanzate, Via Comunale Margherita, 482, 80145, Napoli, Italy
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Middelhaufe S, Garzia L, Ohndorf UM, Kachholz B, Zollo M, Steegborn C. Domain mapping on the human metastasis regulator protein h-Prune reveals a C-terminal dimerization domain. Biochem J 2008; 407:199-205. [PMID: 17655525 PMCID: PMC2049022 DOI: 10.1042/bj20070408] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The human orthologue of the Drosophila prune protein (h-Prune) is an interaction partner and regulator of the metastasis suppressor protein NM23-H1 (non-metastatic protein 23). Studies on a cellular breast-cancer model showed that inhibition of the cAMP-specific PDE (phosphodiesterase) activity of h-Prune lowered the incidence of metastasis formation, suggesting that inhibition of h-Prune could be a therapeutic approach towards metastatic tumours. H-Prune shows no sequence similarity with known mammalian PDEs, but instead appears to belong to the DHH (Asp-His-His) superfamily of phosphoesterases. In order to investigate the structure and molecular function of h-Prune, we expressed recombinant h-Prune in a bacterial system. Through sequence analysis and limited proteolysis, we identified domain boundaries and a potential coiled-coil region in a C-terminal cortexillin homology domain. We found that this C-terminal domain mediated h-Prune homodimerization, as well as its interaction with NM23-H1. The PDE catalytic domain of h-Prune was mapped to the N-terminus and shown to be active, even when present in a monomeric form. Our findings indicate that h-Prune is composed of two independent active sites and two interaction sites for the assembly of oligomeric signalling complexes.
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Affiliation(s)
- Sabine Middelhaufe
- *Department of Physiological Chemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Livia Garzia
- †Centro di Ingegneria Genetica e Biotecnologie Avanzate, 80145 Napoli, Italy
| | - Uta-Maria Ohndorf
- *Department of Physiological Chemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Barbara Kachholz
- *Department of Physiological Chemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Massimo Zollo
- †Centro di Ingegneria Genetica e Biotecnologie Avanzate, 80145 Napoli, Italy
- ‡Dipartimento di Biochimica e Biotecnologie Mediche, Università degli Studi di Napoli “Federico II”, Via Pansini 5, Naples, Italy
| | - Clemens Steegborn
- *Department of Physiological Chemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
- To whom correspondence should be addressed (email )
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Carrera M, Cañas B, Piñeiro C, Vázquez J, Gallardo JM. De Novo Mass Spectrometry Sequencing and Characterization of Species-Specific Peptides from Nucleoside Diphosphate Kinase B for the Classification of Commercial Fish Species Belonging to the Family Merlucciidae. J Proteome Res 2007; 6:3070-80. [PMID: 17622168 DOI: 10.1021/pr0701963] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The characterization by de novo peptide sequencing of the different protein nucleoside diphosphate kinase B (NDK B) from all the commercial hakes and grenadiers belonging to the family Merlucciidae is reported. A classical proteomics approach, consisting of two-dimmensional gel electrophoresis, tryptic in-gel digestion of the excised spots, MALDI-TOF MS, LC-MS/MS, and nanoESI-MS/MS analyses, was followed for the purification and characterization of the different isoforms of the NDK B. Fragmentation spectra were used for de novo peptide sequence. A high degree of homology was found between the sequences of all the species studied and the NDK B sequence from Gillichthys mirabilis, which is accessible in the protein databases. Particular attention was paid to the differential characterization of species-specific peptides that could be used for fish authentication purposes. These findings allowed us to propose a rapid and effective classification method, based in the detection of these biomarker peptides using the selective ion reaction monitoring (SIRM) scan mode in mass spectrometry.
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Affiliation(s)
- Mónica Carrera
- Departamento Tecnología de Alimentos, Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain.
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Xiong S, Qian CW, Huang L, Wang YF, Zhang MY, Li JX, Yan JF, Wang XN, Zhang XW, Bi ZG. [Physical and chemical characters of recombinant human nucleoside diphosphate kinase A]. Sheng Wu Gong Cheng Xue Bao 2004; 20:85-9. [PMID: 16108496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
To purify recombinant human nucleoside diphosphate kinase A (rhNDPK-A) and determine its physical and chemical characters, recombinant NDPK-A producing E. coli was cultured in 80L fermentor under high cell density culture (HCDC) conditions. The harvested cells were treated with high pressure to break the cell up, tangential-flow microfiltration to remove the bacteria debris and ultrafiltration to concentrate the filtered solution containing target protein. The crude NDPK-A was purified by ion exchange chromatography with DEAE Sepharose Fast Flow, affinity chromatography with Cibarcron Blue 3GA Sepharose CL-4B and gel filtration with Sephadex G-100. The purity of rhNDPK-A was analyzed with SDS-PAGE and RP-HPLC. The Enzymatic activity was determined with RP-HPLC. The molecular weight (MW) was measured with matrix assisted laser desorption ionization time-of-flight MS (MALDI-TOF MS). The N-terminal residue was sequenced with Edman method. The apparent molecular weight of rhNDPK-A in solution was determined with multiangle laser light-scattering method (MALS). It was found that the purity of rhNDPK-A was 97.3% with SDS-PAGE method and 99.2% with RP-HPLC method. The specific enzymatic activity was (900 +/- 100) u/mg. The molecular weight was 17017, which was 132 less than the calculated value according to the amino acid sequence of NDPK-A. The sequencing result of rhNDPK-A revealed that its N-terminal residue was Ala, which was the second residue on N-terminal of native NDPK-A. The calculated MW of N-terminal deleted rhNDPK-A was 17017, exactly equal to the experimental value. The result of apparent MW determination revealed that rhNDPK-A formed homohexamer in solution with a MW of 102kD. These results suggested that rhNDPK-A possessed character identical to its native counterpart of assembling into hexamer. Confirming the identity of rhNDPK-A to its native counterpart provided a good foundation for drug development and mechanism study of NDPK-A.
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Affiliation(s)
- Sheng Xiong
- Biomedical Research and Development Center, Jinan University, Guangzhou 510630, China
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