Widespread presence of "bacterial-like" PPP phosphatases in eukaryotes

BMC Evolutionary Biology

Volumn 4, Issue , 2004, Pages

  Andreeva, Alexandra V ^a,b   Kutuzov, Mikhail A ^a,b  

^a OXFORD BROOKES UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF ILLINOIS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGAE; ANIMALIA; ARCHAEA; BACILLARIOPHYTA; BACTERIA (MICROORGANISMS); COLWELLIA; EMBRYOPHYTA; EUKARYOTA; FUNGI; PROTEOBACTERIA; RHIZOBIALES; RHODOBACTERALES; RHODOPHYTA; RHODOSPIRILLACEAE; SHEWANELLA; TRYPANOSOMA; TRYPANOSOMATIDAE; VIRIDIPLANTAE;

ARABIDOPSIS PROTEIN; BACTERIAL PROTEIN; PHOSPHOPROTEIN PHOSPHATASE; SCHIZOSACCHAROMYCES POMBE PROTEIN;

ALPHAPROTEOBACTERIA; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; CHLAMYDOMONAS REINHARDTII; COMPARATIVE STUDY; ENZYMOLOGY; EUKARYOTIC CELL; GENETICS; MOLECULAR GENETICS; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SHEWANELLA; TICK;

ALPHAPROTEOBACTERIA; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; ARABIDOPSIS PROTEINS; BACTERIAL PROTEINS; CHLAMYDOMONAS REINHARDTII; EUKARYOTIC CELLS; MOLECULAR SEQUENCE DATA; PHOSPHOPROTEIN PHOSPHATASES; PROTEIN STRUCTURE, TERTIARY; SCHIZOSACCHAROMYCES POMBE PROTEINS; SHEWANELLA; TICKS;

EID: 12344321762     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-4-47     Document Type: Article

References (65)

1. Cohen PTW: Novel protein serine/threonine phosphatases: Variety is the spice of life. Trends Biochem Sci 1997, 22:245-251.
2. Andreeva AV, Kutuzov MA: RdgC/PP5-related phosphatases: novel components in signal transduction. Cell Signal 1999, 11:555-562.
3. Ariño J: Novel protein phosphatases in yeast. Eur J Biochem 2002, 269:1072-1077.
4. Kerk D, Bulgrien J, Smith DW, Barsam B, Veretnik S, Gribskov M: The complement of protein phosphatase catalytic subunits encoded in the genome of Arabidopsis. Plant Physiol 2002, 129:908-925.
5. Kennelly PJ: Archaeal protein kinases and protein phosphatases: insights from genomics and biochemistry. Biochem J 2003, 370:373-389.
6. Kennelly PJ: Protein phosphatases - a phylogenetic perspective. Chem Rev 2001, 101:2291-2312.
7. Tsuruta H, Aizono Y: Enzymatical properties of psychrophilic phosphatase I. J Biochem 1999, 125:690-695.
8. Tsuruta H, Aizono Y: Cloning of phosphatase I gene from a psychrophile, Shewanella sp, and some properties of the recombinant enzyme. J Biochem 2000, 127:143-149.
9. Iwanicki A, Herman-Antosiewicz A, Pierechod M, Seror SJ, Obuchowski M: PrpE, a PPP protein phosphatase from Bacillus subtilis with unusual substrate specificity. Biochem J 2002, 366:929-936.
10. Koonin EV: Bacterial and bacteriophage protein phosphatases. Mol Microbiol 1993, 8:785-786.
11. Barton GJ, Cohen PTW, Barford D: Conservation analysis and structure prediction of the protein serine/threonine phosphatases. Sequence similarity with diadenosine tetraphosphatase from Escherichia coli suggests homology to the protein phosphatases. Eur J Biochem 1994, 220:225-237.
12. Kennelly PJ: Protein kinases and protein phosphatases in prokaryotes: a genomic perspective. FEMS Microbiol Lett 2002, 206:1-8.
13. Missiakas D, Raina S: Signal transduction pathways in response to protein misfolding in the extracytoplasmic compartments of E.coli : role of two new phosphoprotein phosphatases PrpA and PrpB. EMBO J 1997, 16:1670-1685.
14. Umeyama T, Naruoka A, Horinouchi S: Genetic and biochemical characterization of a protein phosphatase with dual substrate specificity in Streptomyces coelicolor A3(2). Gene 2000, 258:55-62.
15. Shi L: Manganese-dependent protein O-phosphatases in prokaryotes and their biological functions. Front Biosci 2004, 9:1382-1397.
16. Barford D: Molecular mechanisms of the protein serine/threonine phosphatases. Trends Biochem Sci 1996, 21:407-412.
17. Andreeva AV, Kutuzov MA: Physcomitrella patens gene/cDNA fragments related to genes encoding protein Ser/Thr phosphatases. J Plant Physiol 1999, 155:153-158.
18. Haas BJ, Volfovsky N, Town CD, Troukhan M, Alexandrov N, Feldmann KA, Flavell RB, White O, Salzberg SL: Full-length messenger RNA sequences greatly improve genome annotation. Genome Biol 2002, 3:research0029..
19. Voegtli WC, White DJ, Reiter NJ, Rusnak F, Rosenzweig AC: Structure of the bacteriophage λ Ser/Thr protein phosphatase with sulfate ion bound in two coordination modes. Biochemistry 2000, 39:15365-15374.
20. Egloff MP, Cohen PTW, Reinemer P, Barford D: Crystal structure of the catalytic subunit of human protein phosphatase 1 and its complex with tungstate. J Mol Biol 1995, 254:942-959.
21. Goldberg J, Huang HB, Kwon YG, Greengard P, Nairn AC, Kuriyan J: Three-dimensional structure of the catalytic subunit of protein serine/threonine phosphatase-1. Nature 1995, 376:745-753.
22. Kissinger CR, Parge HE, Knighton DR, Lewis CT, Pelletier LA, Tempczyk A, Kalish VJ, Tucker KD, Showalter RE, Moomaw EW, Gastinel LN, Habuka N, Chen X, Maldonado F, Barker JE, Bacquet R, Villafranca JE: Crystal structures of human calcineurin and the human FKBP12-FK506-calcineurin complex. Nature 1995, 378:641-644.
23. Coster F, van Dyck L, Jonniaux J-L, Purnelle B, Goffeau A: The sequence of a 13.5 kb DNA segment from the left arm of yeast chromosome XIV reveals MER1; RAP1; a new putative member of the DNA replication complex and a new putative serine/threonine phosphatase gene. Yeast 1995, 11:85-91.
24. Zhang J, Zhang Z, Brew K, Lee EYC: Mutational analysis of the catalytic subunit of muscle protein phosphatase-1. Biochemistry 1996, 35:6276-6282.
25. Andreeva AV, Kutuzov MA: PPP family of protein Ser/Thr phosphatases: Two distinct branches? Mol Biol Evol 2001, 18:448-452.
26. Felsenstein J: PHYLIP (phylogeny inference package). Version 3.5731999 Distributed by the author, Department of Genetics, University of Washington, Seattle .
27. Huson DH, Bryant D: Estimating phylogenetic trees and networks using SplitsTree4, in preparation. .
28. Schmidt HA, Strimmer K, Vingron M, von Haeseler A: TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 2002, 18:502-504.
29. Bryant D, Moulton V: Neighbor-Net: An agglomerative method for the construction of phylogenetic networks. Mol Biol Evol 2004, 21:255-65.
30. Connor JH, Kleeman T, Barik S, Honkanen RE, Shenolikar S: Importance of the β12-β13 loop in protein phosphatase-1 catalytic subunit for inhibition by toxins and mammalian protein inhibitors. J Biol Chem 1999, 274:22366-22372.
31. Lee EY, Zhang L, Zhao S, Wei Q, Zhang J, Qi ZQ, Belmonte ER: Phosphorylase phosphatase: new horizons for an old enzyme. Front Biosci 1999, 4:D270-D285.
32. Watanabe T, Huang HB, Horiuchi A, da Cruze Silva EF, Hsieh-Wilson L, Allen PB, Shenolikar S, Greengard P, Nairn AC: Protein phosphatase 1 regulation by inhibitors and targeting subunits. Proc Natl Acad Sci USA 2001, 98:3080-3085.
33. Sprent JI: Evolution and diversity in the legume-rhizobium symbiosis: Chaos theory? In In Symbiotic Nitrogen Fixation Edited by: Graham PH, Sadowsky MJ, Vance CP. Dordrecht: Kluwer Academic Publishers; 1994:1-10.
34. Fleischman D, Kramer D: Photosynthetic rhizobia. Biochim Biophys Acta 1998, 1364:17-36.
35. Escobar MA, Dandekar AM: Agrobacterium tumefaciens as an agent of disease. Trends Plant Sci 2003, 8:380-386.
36. Kunik T, Tzfira T, Kapulnik Y, Gafni Y, Dingwall C, Citovsky V: Genetic transformation of HeLa cells by Agrobacterium. Proc Natl Acad Sci USA 2001, 98:1871-1876.
37. Scholl EH, Thorne JL, McCarter JP, Bird DM: Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach. Genome Biol 2003, 4:R39.
38. Hannaert V, Saavedra E, Duffieux F, Szikora JP, Rigden DJ, Michels PA, Opperdoes FR: Plant-like traits associated with metabolism of Trypanosoma parasites. Proc Natl Acad Sci USA 2003, 100:1067-1071.
39. Foth BJ, McFadden GI: The apicoplast: a plastid in Plasmodium falciparum and other Apicomplexan parasites. Int Rev Cytol 2003, 224:57-110.
40. Hast T, Follmann H: Identification of two thylakoid-associated phosphatases with protein phosphatase activity in chloroplasts of the soybean (Glycine max). J Photochem Photobiol B -Biology 1996, 36:313-319.
41. Hammer MF, Markwell J, Sarath G: Purification of a protein phosphatase from chloroplast stroma capable of dephosphorylating the light-harvesting complex-II. Plant Physiol 1997, 113:227-233.
42. Kisselev LL, Justesen J, Wolfson AD, Frolova LY: Diadenosine oligophosphates (Ap(n)A), a novel class of signalling molecules? FEBS Lett 1998, 427:157-163.
43. Vartanian AA, Suzuki H, Poletaev AI: The involvement of diadenosine 5 ′,5 ‴'-P-1,P-4-tetraphosphate in cell cycle arrest and regulation of apoptosis. Biochem Pharmacol 2003, 65:227-235.
44. Pekarsky Y, Zanesi N, Palamarchuk A, Huebner K, Croce CM: FHIT: from gene discovery to cancer treatment and prevention. Lancet Oncology 2002, 3:748-754.
45. Chan CP, Gallis B, Blumenthal DK, Pallen CJ, Wang JH, Krebs EG: Characterization of the phosphotyrosyl protein phosphatase activity of calmodulin-dependent protein phosphatase. J Biol Chem 1986, 261:9890-9895.
46. MacKintosh C, Garton AJ, McDonnell A, Barford D, Cohen PTW, Tonks NK, Cohen P: Further evidence that inhibitor-2 acts like a chaperone to fold PP1 into its native conformation. FEBS Lett 1996, 397:235-238.
47. Zhuo S, Clemens JC, Hakes DJ, Barford D, Dixon JE: Expression, purification, crystallization, and biochemical characterization of a recombinant protein phosphatase. J Biol Chem 1993, 268:17754-17761.
48. Shi L, Carmichael WW, Kennelly PJ: Cyanobacterial PPP family protein phosphatases possess multifunctional capabilities and are resistant to microcystin-LR. J Biol Chem 1999, 274:10039-10046.
49. Shi L, Kehres DG, Maguire ME: The PPP-family protein phosphatases PrpA and PrpB of Salmonella enterica serovar Typhimurium possess distinct biochemical properties. J Bacteriol 2001, 183:7053-7057.
50. Luan S: Protein phosphatases in plants. Annu Rev Plant Biol 2003, 54:63-92.
51. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997, 25:3389-3402.
52. NCBI Blast search [http://www.ncbi.nlm.nih.gov/blast]
53. NCBI BLAST with eukaryotic genomes [http:// www.ncbi.nlm.nih.gov/sutils/ genom_tree.cgi?organism=euk]
54. Fungal Genomes Blast search at the Broad Institute [http:// www.broad.mit.edu/cgi-bin/annotation/fgi/blast_page.cgi]
55. The Arabidopsis Information Resource (TAIR) Blast search [http://www.arabidopsis.org/Blast]
56. Gene Index databases of tentative consensus sequences at the Institute for Genomic Research (TIGR) [http:// www.tigr.org/tdb]
57. Chlamydomonas reinhardtii draft genome BLAST search [http://aluminum.jgi- psf.org/prod/bin/runBlast.pl?db=chlre1]
58. NCBI Taxonomy Homepage [http://www.ncbi.nlm.nih.gov/Tax onomy/taxonomyhome.html]
59. Higgins DG, Thompson JD, Gibson TJ: Using CLUSTAL for multiple sequence alignments. Methods Enzymol 1996, 266:383-402.
60. CLUSTAL W: Multiple Sequence Alignment at Kyoto University Bioinformatics Centre. [http://clustalw.genome.ad.jp].
61. Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4:406-425.
62. SplitsTree: Analyzing and Visualizing Evolutionary Data. [http://www-ab.informatik.uni-tuebingen.de/software/splits/ welcome_en.html].
63. Emanuelsson O, Nielsen H, Brunak S, von Heijne G: Predicting subcellular localization of proteins based on their N-terminal amino acid sequence. J Mol Biol 2000, 300:1005-1016.
64. TargetP Server at the Centre for Biological Sequence Analysis, Technical University of Denmark [http://www.cbs.dtu.dk/ services/TargetP]
65. Chlamydomonas reinhardtii draft genome, scaffold 45 [http:genome.jgi-psf. org/cgi-bin/getScaffold?db=chlre1&scaf fold=scaffold_45]