Nme protein family evolutionary history, a vertebrate perspective

BMC Evolutionary Biology

Volumn 9, Issue 1, 2009, Pages

  Desvignes, Thomas ^a,b   Pontarotti, Pierre ^c   Fauvel, Christian ^b   Bobe, Julien ^a  

^a Parc Scientifique de Luminy   (France)

^b IFREMER   (France)

^c AIX MARSEILLE UNIVERSITY   (France)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEOSIDE DIPHOSPHATE KINASE NM23;

AMINO ACID SEQUENCE; ARTICLE; HUMAN; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PHYLOGENETIC TREE; PROTEIN DOMAIN; PROTEIN FAMILY; SEQUENCE ALIGNMENT; SPECIES DIFFERENCE; ANIMAL; CHEMISTRY; GENETICS; MOLECULAR GENETICS; PHYLOGENY; VERTEBRATE;

DANIO RERIO; MAMMALIA; TELEOSTEI; VERTEBRATA;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; HUMANS; MOLECULAR SEQUENCE DATA; NM23 NUCLEOSIDE DIPHOSPHATE KINASES; PHYLOGENY; SEQUENCE ALIGNMENT; VERTEBRATES;

EID: 72449187617     PISSN: None     EISSN: 14712148     Source Type: Journal    
DOI: 10.1186/1471-2148-9-256     Document Type: Article

References (90)

1. Some reactions of adenosine and inosine phosphates in animal tissues. HA Krebs R Hems, Biochim Biophys Acta 1953 12 172 180 10.1016/0006-3002(53)90136-X 13115426
2. Transphosphorylation between Nucleoside Polyphosphates. P Berg WK Jok Lik, Nature 1953 172 1008 1009 10.1038/1721008a0 13111245
3. Nucleoside diphosphate kinase from Myxococcus xanthus. I. Cloning and sequencing of the gene. J Munoz-Dorado M Inouye S Inouye, J Biol Chem 1990 265 2702 2706 2154455
4. Nucleoside diphosphate kinase from Myxococcus xanthus. II. Biochemical characterization. J Munoz-Dorado S Inouye M Inouye, J Biol Chem 1990 265 2707 2712 2154456
5. Functional cloning of a nucleoside diphosphate kinase from Dictyostelium discoideum. ML Lacombe V Wallet H Troll M Veron, J Biol Chem 1990 265 10012 10018 2161830
6. Isolation and characterization of a cDNA clone encoding rat nucleoside diphosphate kinase. N Kimura N Shimada K Nomura K Watanabe, J Biol Chem 1990 265 15744 15749 2168422
7. A gene network for navigating the literature. R Hoffmann A Valencia, Nat Genet 2004 36 664 10.1038/ng0704-664 15226743
8. The Mouse Genome Database (MGD): mouse biology and model systems. CJ Bult JT Eppig JA Kadin JE Richardson JA Blake the Mouse Genome Database Group, Nucl Acids Res 2008 36 724 D728 10.1093/nar/gkm961 18158299
9. HUGO Gene Nomenclature Committee at the European Bioinformatics Institute. http://www.genenames.org
10. The Rat Genome Database, update 2007 - easing the path from disease to data and back again. SN Twigger M Shimoyama S Bromberg AE Kwitek HJ Jacob, Nucleic Acids Res 2007 35 658 D662 10.1093/nar/gkl988 17151068
11. Evidence for a Novel Gene Associated With Low Tumor Metastatic Potential. PS Steeg G Bevilacqua L Kopper UP Thorgeirsson JE Talmadge LA Liotta, et al. J Natl Cancer Inst 1988 80 200 204 10.1093/jnci/80.3.200 3346912
12. Analysis of the lethal interaction between the prune and Killer of prune mutations of Drosophila. J Biggs N Tripoulas E Hersperger C Dearolf A Shearn, Genes & Development 1988 2 1333 1343 10.1101/gad.2.10.1333 2849580
13. Nucleoside diphosphate kinase from Escherichia coli; its overproduction and sequence comparison with eukaryotic enzymes. H Hama N Almaula CG Lerner S Inouye M Inouye, Gene 1991 105 31 36 10.1016/0378-1119(91)90510-I 1657712
14. Reduced Nm23/Awd protein in tumour metastasis and aberrant Drosophila development. AM Rosengard HC Krutzsch A Shearn JR Biggs E Barker IMK Margulies, et al. Nature 1989 342 177 180 10.1038/342177a0 2509941
15. The human Nm23/nucleoside diphosphate kinases. ML Lacombe L Milon A Munier JG Mehus DO Lambeth, Journal of Bioenergetics and Biomembranes 2000 32 247 258 10.1023/A:1005584929050 11768308
16. Inhibition of progesterone-induced Xenopus oocyte maturation by Nm23. SY Kim JE Ferrell SK Chae KJ Lee, Cell Growth & Differentiation 2000 11 485 490
17. Differential expression of nucleoside diphosphate kinases (NDPK/NM23) during Xenopus early development. T Ouatas M Selo Z Sadji J Hourdry H Denis A Mazabraud, International Journal of Developmental Biology 1998 42 43 52 9496785
18. Molecular cloning of an Atlantic salmon nucleoside diphosphate kinase cDNA and its pattern of expression during embryogenesis. M Murphy T Harte J McInerney TJ Smith, Gene 2000 257 139 148 10.1016/S0378-1119(00)00374-7 11054576
19. Cloning and characterization of cDNA encoding zebrafish Danio rerio NM23-B gene. JS Lee SH Lee, Gene 2000 245 75 79 10.1016/S0378-1119(00)00037-8 10713447
20. Three different genes encode NM23 nucleoside diphosphate kinases in Xenopus laevis. T Ouatas B Abdallah L Gasmi J Bourdais E Postel A Mazabraud, Gene 1997 194 215 225 10.1016/S0378-1119(97)00160-1 9272863
21. Molecular evolution of nucleoside diphosphate kinase genes: Conserved core structures and multiple-layered regulatory regions. N Ishikawa N Shimada Y Takagi Y Ishijima M Fukuda N Kimura, Journal of Bioenergetics and Biomembranes 2003 35 7 18 10.1023/A:1023433504713 12848337
22. Separate nuclear genes encode cytosolic and mitochondrial nucleoside diphosphate kinase in Dictyostelium discoideum. H Troll T Winckler I Lascu N Muller W Saurin M Veron, et al. J Biol Chem 1993 268 25469 25475 8244981
23. CDD: specific functional annotation with the Conserved Domain Database. A Marchler-Bauer JB Anderson F Chitsaz MK Derbyshire C DeWeese-Scott JH Fong, et al. Nucl Acids Res 2009 37 205 D210 18984618 10.1093/nar/gkn845
24. The mammalian Nm23/NDPK family: from metastasis control to cilia movement. M Boissan S Dabernat E Peuchant U Schlattner I Lascu ML Lacombe, Mol Cell Biochem 2009 329 51 62 10.1007/s11010-009-0120-7 19387795
25. Sptrx-2, a fusion protein composed of one thioredoxin and three tandemly repeated NDP-kinase domains is expressed in human testis germ cells. CM Sadek AE Damdimopoulos M Pelto-Huikko JA Gustafsson G Spyrou A Miranda-Vizuete, Genes Cells 2001 6 1077 1090 10.1046/j.1365-2443.2001.00484.x 11737268
26. Read-through transcript from NM23-H1 into the neighboring NM23-H2 gene encodes a novel protein, NM23-LV. LJ Valentijn J Koster R Versteeg, Genomics 2006 87 483 489 10.1016/j.ygeno.2005.11.004 16442775
27. Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Y Nakatani H Takeda Y Kohara S Morishita, Genome Research 2007 17 1254 1265 17652425 10.1101/gr.6316407 (Pubitemid 47360900)
28. DOE Joint Genome Institute. http://www.jgi.doe.gov/
29. Human c-myc transcription factor PuF identified as nm23-H2 nucleoside diphosphate kinase, a candidate suppressor of tumor metastasis. EH Postel SJ Berberich SJ Flint CA Ferrone, Science 1993 261 478 480 10.1126/science.8392752 8392752
30. Molecular cloning and functional expression of the second mouse nm23/NDP kinase gene, nm23-M2. T Urano K Takamiya K Furukawa H Shiku, Febs Letters 1992 309 358 362 10.1016/0014-5793(92)80807-S 1325378
31. Nucleoside Diphosphate Kinase from Bovine Retina: Purification, Subcellular Localization, Molecular Cloning, and Three-Dimensional Structure NG Abdulaev GN Karaschuk JE Ladner DL Kakuev AV Yakhyaev M Tordova, et al. Biochemistry 1998 37 13958 13967 10.1021/bi980853s 9760230
32. Molecular cloning and analysis of function of nucleoside diphosphate kinase (NDPK) from the scallop Chlamys farreri. XZ Shi XF Zhao JX Wang, Biochemistry (Mosc) 2008 73 686 692 10.1134/S0006297908060096 18620535
33. A Drosophila gene that is homologous to a mammalian gene associated with tumor metastasis codes for a nucleoside diphosphate kinase. J Biggs E Hersperger PS Steeg LA Liotta A Shearn, Cell 1990 63 933 940 10.1016/0092-8674(90)90496-2 2175255
34. Cloning and Functional Analysis of the ndk1 Gene Encoding Nucleoside-diphosphate Kinase in Schizosaccharomyces pombe. H Izumiya M Yamamoto, J Biol Chem 1995 270 27859 27864 10.1074/jbc.270.46.27859 7499258
35. Cloning and characterisation of a pea mitochondrial NDPK. ML Escobar Galvis G Hakansson K Alexciev C Knorpp, Biochimie 1999 81 1089 1096 10.1016/S0300-9084(99)00353-3 10607403
36. Characterization of the 3' - 5' Exonuclease Activity Found in Human Nucleoside Diphosphate Kinase 1 (NDK1) and Several of Its Homologues. JH Yoon P Singh DH Lee J Qiu S Cai TR O'Connor, et al. Biochemistry 2005 44 15774 15786 16313181 10.1021/bi0515974 (Pubitemid 41746909)
37. The Crystal Structure of Human Nucleoside Diphosphate Kinase, NM23-H2. PA Webb O Perisic CE Mendola JM Backer RL Williams, Journal of Molecular Biology 1995 251 574 587 10.1006/jmbi.1995.0457 7658474
38. The catalytic mechanism of nucleoside diphosphate kinases. I Lascu P Gonin, J Bioenerg Biomembr 2000 32 237 246 10.1023/A:1005532912212 11768307 (Pubitemid 30727488)
39. A second form (beta isoform) of nucleoside diphosphate kinase from rat. Isolation and characterization of complementary and genomic DNA and expression. N Shimada N Ishikawa Y Munakata T Toda K Watanabe N Kimura, J Biol Chem 1993 268 2583 2589 8381409
40. Cloning of a second nm23-M1 cDNA: expression in the central nervous system of adult mouse and comparison with nm23-M2 mRNA distribution. S Dabernat M Larou K Masse T Hokfelt G Mayer JY Daniel, et al. Brain Res Mol Brain Res 1999 63 351 365 10.1016/S0169-328X(98)00300-3 9878823
41. Organization and expression of mouse nm23-M1 gene. Comparison with nm23-M2 expression. S Dabernat M Larou K Masse E Dobremez M Landry C Mathieu, et al. Gene 1999 236 221 230 10.1016/S0378-1119(99)00288-7 10452942
42. Embryonic Expression of Nm23 During Mouse Organogenesis. M Lakso PS Steeg H Westphal, Cell Growth & Differentiation 1992 3 873 879
43. Evolution by gene duplication: an update. J Zhang, Trends in Ecology & Evolution 2003 18 292 298 10.1016/S0169-5347(03)00033-8 (Pubitemid 36631749)
44. Consequences of lineage-specific gene loss on functional evolution of surviving paralogs: ALDH1A and retinoic acid signaling in vertebrate genomes. C Canestro JM Catchen A Rodriguez-Mari H Yokoi JH Postlethwait, PLoS Genet 2009 5 1000496 19478994 10.1371/journal.pgen.1000496
45. PuF/NM23-H2/NDPK-B transactivates a human c-myc promoter-CAT gene via a functional nuclease hypersensitive element. SJ Berberich EH Postel, Oncogene 1995 10 2343 2347 7784082
46. Identification of a Second Human nm23 Gene, nm23-H2. JA Stahl A Leone AM Rosengard L Porter CR King PS Steeg, Cancer Res 1991 51 445 449 1988104
47. Nm23-M2/NDP kinase B induces endogenous c-myc and nm23-M1/NDP kinase A overexpression in BAF3 cells. Both NDP kinases protect the cells from oxidative stress-induced death. S Arnaud-Dabernat K Masse M Smani E Peuchant M Landry PM Bourbon, et al. Exp Cell Res 2004 301 293 304 10.1016/j.yexcr.2004.07.026 15530864
48. Discovery of NM23-H2 as an estrogen receptor beta-associated protein: role in estrogen-induced gene transcription and cell migration. K Rayner YX Chen B Hibbert D White H Miller EH Postel, et al. J Steroid Biochem Mol Biol 2008 108 72 81 10.1016/j.jsbmb.2007.07.006 17964137
49. Human NM23/nucleoside diphosphate kinase regulates gene expression through DNA binding to nuclease-hypersensitive transcriptional elements. EH Postel SJ Berberich JW Rooney DM Kaetzel, J Bioenerg Biomembr 2000 32 277 284 10.1023/A:1005541114029 11768311
50. Overexpression of DR-nm23, a protein encoded by a member of the nm23 gene family, inhibits granulocyte differentiation and induces apoptosis in 32Dc13 myeloid cells. D Venturelli R Martinez P Melotti I Casella C Peschle C Cucco, et al. Proceedings of the National Academy of Sciences of the United States of America 1995 92 7435 7439 7638209 10.1073/pnas.92.16.7435
51. Gene Structure, Promoter Activity, and Chromosomal Location of the DR-nm23 Gene, a Related Member of the nm23 Gene Family. R Martinez D Venturelli D Perrotti ML Veronese K Kastury T Druck, et al. Cancer Res 1997 57 1180 1187 9067290
52. Structural and catalytic properties and homology modelling of the human nucleoside diphosphate kinase C, product of the DRnm23 gene. M Erent P Gonin J Cherfils P Tissier G Raschella A Giartosio, et al. Eur J Biochem 2001 268 1972 1981 10.1046/j.1432-1327.2001.2076.doc.x 11277919
53. Characterization of the nm23-M2, nm23-M3 and nm23-M4 mouse genes: comparison with their human orthologs. K Masse S Dabernat PM Bourbon M Larou L Amrein P Barraud, et al. Gene 2002 296 87 97 10.1016/S0378-1119(02)00836-3 12383506
54. Expression patterns of nm23 genes during mouse organogenesis. L Amrein P Barraud JY Daniel Y Perel M Landry, Cell Tissue Res 2005 322 365 378 10.1007/s00441-005-0036-9 16082520
55. Xenopus NM23-X4 regulates retinal gliogenesis through interaction with p27Xic1. T Mochizuki A Bilitou C Waters K Hussain M Zollo Si Ohnuma, Neural Development 2009 4 1 19123928 10.1186/1749-8104-4-1
56. The Nucleoside Diphosphate Kinase Activity of DRnm23 Is Not Required for Inhibition of Differentiation and Induction of Apoptosis in 32Dcl3 Myeloid Precursor Cells. D Venturelli V Cesi S Ransac A Engelhard D Perrotti B Calabretta, Experimental Cell Research 2000 257 265 271 10.1006/excr.2000.4899 10837140
57. Neuroblastoma specific effects of DR-nm23 and its mutant forms on differentiation and apoptosis. A Negroni D Venturelli B Tanno R Amendola S Ransac V Cesi, et al. Cell Death Differ 2000 7 843 850 10.1038/sj.cdd.4400720 11042679
58. DR-nm23 gene expression in neuroblastoma cells: relationship to integrin expression, adhesion characteristics, and differentiation. R Amendola R Martinez A Negroni D Venturelli B Tanno B Calabretta, et al. J Natl Cancer Inst 1997 89 1300 1310 10.1093/jnci/89.17.1300 9293921
59. Identification of Estrogen-responsive Genes Using a Genome-wide Analysis of Promoter Elements for Transcription Factor Binding Sites. S Kamalakaran SK Radhakrishnan WT Beck, J Biol Chem 2005 280 21491 21497 10.1074/jbc.M409176200 15790569
60. nm23-H4, a new member of the family of human nm23 nucleoside diphosphate kinase genes localised on chromosome 16p13. L Milon MF RousseauMerck A Munier M Erent I Lascu J Capeau, et al. Human Genetics 1997 99 550 557 10.1007/s004390050405 9099850
61. Characterization and Cloning of a Nucleoside-diphosphate Kinase Targeted to Matrix of Mitochondria in Pigeon. DO Lambeth JG Mehus MA Ivey BI Milavetz, J Biol Chem 1997 272 24604 24611 10.1074/jbc.272.39.24604 9305928
62. The Human nm23-H4 Gene Product Is a Mitochondrial Nucleoside Diphosphate Kinase. L Milon P Meyer M Chiadmi A Munier M Johansson A Karlsson, et al. J Biol Chem 2000 275 14264 14272 10.1074/jbc.275.19.14264 10799505
63. The Nucleoside Diphosphate Kinase D (NM23-H4) Binds the Inner Mitochondrial Membrane with High Affinity to Cardiolipin and Couples Nucleotide Transfer with Respiration. M Tokarska-Schlattner M Boissan A Munier C Borot C Mailleau O Speer, et al. J Biol Chem 2008 283 26198 26207 10.1074/jbc.M803132200 18635542
64. Phosphorylation of adenosine monophosphate in the mitochondrial matrix. HA Krebs D Wiggins, Biochem J 1978 174 297 301 697756
65. What is the function of GTP produced in the Krebs citric acid cycle? DO Lambeth, IUBMB Life 2002 54 143 144 10.1080/15216540214539 12489642
66. GTP in the mitochondrial matrix plays a crucial role in organellar iron homoeostasis1. D Gordon E Lyver E Lesuisse A Dancis D Pain, Biochem J 2006 400 163 168 16842238 10.1042/BJ20060904 (Pubitemid 44763831)
67. RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree. M Robinson-Rechavi D Huchon, Bioinformatics 2000 16 296 297 10.1093/bioinformatics/16.3.296 10869026
68. A new human nm23 homologue (nm23-H5) specifically expressed in testis germinal cells. A Munier C Feral L Milon VPB Pinon G Gyapay J Capeau, et al. Febs Letters 1998 434 289 294 10.1016/S0014-5793(98)00996-X 9742940
69. Cloning, sequencing, and characterization of the murine nm23-M5 gene during mouse spermatogenesis and spermiogenesis. KC Hwang DW Ok JC Hong MO Kim JH Kim, Biochemical and Biophysical Research Communications 2003 306 198 207 10.1016/S0006-291X(03)00916-1 12788088
70. Nm23/NDP kinases in human male germ cells: role in spermiogenesis and sperm motility? A Munier C Serres ML Kann M Boissan C Lesaffre J Capeau, et al. Experimental Cell Research 2003 289 295 306 10.1016/S0014-4827(03)00268-4 14499630
71. Nm23-M5 mediates round and elongated spermatid survival by regulating GPX-5 levels. YJ Choi SK Cho KC Hwang C Park JH kim SB Park, et al. Febs Letters 2009 583 1292 1298 10.1016/j.febslet.2009.03.023 19303412
72. NME6: a new member of the nm23/nucleoside diphosphate kinase gene family located on human chromosome 3p21.3. JG Mehus P Deloukas DO Lambeth, Human Genetics 1999 104 454 459 10.1007/s004390050987 10453732
73. A novel human nucleoside diphosphate (NDP) kinase, Nm23-H6, localizes in mitochondria and affects cytokinesis. H Tsuiki M Nitta A Furuya N Hanai T Fujiwara M Inagaki, et al. J Cell Biochem 1999 76 254 269 10.1002/(SICI)1097- 4644(20000201)76:2<254::AID-JCB9>3.0.CO;2-G 10618642
74. Axonemal protofilament ribbons, DM10 domains, and the link to juvenile myoclonic epilepsy. SM King, Cell Motil Cytoskeleton 2006 63 245 253 10.1002/cm.20129 16572395
75. Cloning and Developmental Analysis of Murid Spermatid-specific Thioredoxin-2 (SPTRX-2), a Novel Sperm Fibrous Sheath Protein and Autoantigen. A Miranda-Vizuete K Tsang Y Yu A Jimenez M Pelto-Huikko CJ Flickinger, et al. J Biol Chem 2003 278 44874 44885 10.1074/jbc.M305475200 12909633
76. Molecular cloning and characterization of a thioredoxin/nucleoside diphosphate kinase related dynein intermediate chain from the ascidian, Ciona intestinalis. P Padma A Hozumi K Ogawa K Inaba, Gene 2001 275 177 183 10.1016/S0378-1119(01)00661-8 11574167
77. Characterization of Human Thioredoxin-like 2. A novel microtubule-binding thioredoxin expressed predominantly in the cilia of lung airway epithelium and spermatid manchette and axoneme. CM Sadek A Jimenez AE Damdimopoulos T Kieselbach M Nord JA Gustafsson, et al. J Biol Chem 2003 278 13133 13142 10.1074/jbc.M300369200 12569107
78. Is outer arm dynein intermediate chain 1 multifunctional? K Ogawa H Takai A Ogiwara E Yokota T Shimizu K Inaba, et al. Mol Biol Cell 1996 7 1895 1907 8970153
79. A common variant in combination with a nonsense mutation in a member of the thioredoxin family causes primary ciliary dyskinesia. B+ Duriez P Duquesnoy E Escudier AM Bridoux D Escalier I Rayet, et al. Proceedings of the National Academy of Sciences 2007 104 3336 3341 10.1073/pnas.0611405104 (Pubitemid 46364160)
80. The retinitis pigmentosa-mutated RP2 protein exhibits exonuclease activity and translocates to the nucleus in response to DNA damage. JH Yoon J Qiu S Cai Y Chen ME Cheetham B Shen, et al. Experimental Cell Research 2006 312 1323 1334 10.1016/j.yexcr.2005.12.026 16457815
81. Positional cloning of the gene for X-linked retinitis pigmentosa 2. U Schwahn S Lenzner J Dong S Feil B Hinzmann G van Duijnhoven, et al. Nat Genet 1998 19 327 332 10.1038/1214 9697692
82. NCBI Basic Local Alignment Search Tool (BLAST). http://blast.ncbi.nlm. nih.gov/Blast.cgi
83. Ensembl 2009. TJP Hubbard BL Aken S Ayling B Ballester K Beal E Bragin, et al. Nucl Acids Res 2009 37 690 D697 19033362 10.1093/nar/gkn828
84. The Human Genome Browser at UCSC. WJ Kent CW Sugnet TS Furey KM Roskin TH Pringle AM Zahler, et al. Genome Research 2002 12 996 1006 12045153
85. BLAT-The BLAST-Like Alignment Tool. WJ Kent, Genome Research 2002 12 656 664 11932250
86. MUSCLE: multiple sequence alignment with high accuracy and high throughput. RC Edgar, Nucl Acids Res 2004 32 1792 1797 15034147 10.1093/nar/gkh340 (Pubitemid 38832724)
87. FIGENIX: Intelligent automation of genomic annotation: expertise integration in a new software platform. P Gouret V Vitiello N Balandraud A Gilles P Pontarotti E Danchin, BMC Bioinformatics 2005 6 198 16083500 10.1186/1471-2105-6-198 (Pubitemid 41372468)
88. CASSIOPE: An expert system for conserved regions searches. V Rascol A Levasseur O Chabrol S Grusea P Gouret E Danchin, et al. BMC Bioinformatics 2009 10 284 19740451 10.1186/1471-2105-10-284
89. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. AJ Vilella J Severin A Ureta-Vidal L Heng R Durbin E Birney, Genome Research 2009 19 327 335 19029536 10.1101/gr.073585.107
90. Targeted Gene Expression Profiling in the Rainbow Trout (Oncorhynchus mykiss) Ovary During Maturational Competence Acquisition and Oocyte Maturation. J Bobe T Nguyen B Jalabert, Biol Reprod 2004 71 73 82 10.1095/biolreprod.103. 025205 14985246