Conserved sequence motifs among bacterial, eukaryotic, and archaeal phosphatases that define a new phosphohydrolase superfamily

Protein Science

Volumn 7, Issue 7, 1998, Pages 1647-1652

  Thaller, Maria Cristina ^a,b   Schippa, Serena ^b   Rossolini, Gian Maria ^c  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b SAPIENZA UNIVERSITY OF ROME   (Italy)

^c UNIVERSITY OF SIENA   (Italy)

Author keywords

Acid phosphatase; Homology; Molecular family; Molecular superfamily; Phosphatase; Sequence motif

Indexed keywords

ACID PHOSPHATASE;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL COLONIZATION; DATA BASE; ENZYME ACTIVITY; EUKARYOTE; GENE CLUSTER; PLANT; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

ARCHAEA; BACTERIA (MICROORGANISMS); EUKARYOTA;

EID: 0031820043     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070722     Document Type: Article

References (49)

1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990. Basic alignment search tool. J Mol Biol 215:403-410.
2. Appel RD, Bairoch A, Hochstrasser DF. 1994. A new generation of information retrieval tools for biologists: The example of the ExPASy WWW server. Trends Biochem Sci 19:258-260.
3. Bairoch A, Bucher P, Hofmann K. 1995. The PROSITE database, its status in 1995. Nucleic Acids Res 24:189-196.
4. Bhargava T, Datta S, Ramachandran V, Ramakrishnan R, Roy RK, Sankaran K, Subrahmanyam YVBK. 1995. Virulent Shigella codes for a soluble apyrase: Identification, characterization and cloning of the gene. Curr Sci 68:293-300.
5. Blattner FR, Plunkett G III, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y. 1997. The complete genome sequence of Escherichia coli K-12. Science 277:1453-1462.
6. Borgia PT, Miao Y, Dodge CL. 1996. The orlA gene from Aspergillus nidulans encodes a trehalose-6-phosphate phosphatase necessary to normal growth and chitin synthesis at elevated temperatures. Mol Microbiol 20:1287-1296.
7. Bork P, Ouzounis C, Casari G, Schneider R, Sander C, Dolan M, Gilbert W, Gillevet PM. 1995. Exploring the Mycoplasma capricolum genome: A minimal cell reveals its physiology. Mol Microbiol 16:955-967.
8. Boyer PD, Lardy H, Mayback K, eds. 1961. The enzymes, vol. V. New York: Academic Press.
9. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, Fitzgerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NSM, Weidman JF, Fuhrmann JL, Presley EA, Nguyen D, Utterback TR, Kelley JM, Peterson JD, Sadow PW, Hanna MC, Cotton MD, Hurst MA, Roberts KM, Kaine BP, Borodovsky M, Klenk HP, Fraser CM, Smith HO, Woese CR, Venter JC. 1996. Complete genome sequence of the methanogenic archaeon Methanococcus jannaschii. Science 273:1058-1073.
10. Burland VD, Plunkett G, Daniels DL, Blattner FR. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: Organizational symmetry around the origin of replication. Genomics 16:551-561.
11. Carlomagno MS, Chiariotti L, Alifano P, Nappo AG, Bruni CB. 1988. Structure and function of the Salmonella typhimurium and Escherichia coli K-12 histidine operons. J Mol Biol 203:585-606.
12. Chiariotti L, Nappo AG, Carlomagno MS, Bruni CB. 1986. Gene structure in the histidine operon of Escherichia coli. Identification and nucleotide sequence of the hisB gene. Mol Gen Genet 202:42-47.
13. Collet JF, Gerin I, Rider MH, Veiga-da-Cunha M, Van Schaftingen E. 1997. Human phosphoserine phosphatase: Sequence, expression and evidence for a phosphoenzyme intermediate. FEBS Lett 408:281-284.
14. Daniels DL, Plunkett G III, Burland V, Blattner FR. 1992. Analysis of the Escherichia coli genome: DNA sequence of the region from 84.5 to 86.5 minutes. Science 257:771-778.
15. Davis RE, Hardwick C, Tavernier P, Hodgson S, Singh H. 1995. RNA trans-splicing in flatworms. Analysis of trans-spliced mRNAs and genes in the human parasite, Schistosoma mansoni. J Biol Chem 270:21813-21819.
16. De Virgilio C, Burckert N, Bell W, Jenoe P, Boller T, Wiemken A. 1993. Disraption of TPS2, the gene encoding the 100 kDa subunit of the trehalose-6-phosphate synthase/phosphatase complex in Saccharomyces cerevisiae causes accumulation of trehalose-6-phosphate and loss of trehalose-6-phosphate phosphatase activity. Eur J Biochem 212:315-323.
17. Fleischmann RD, Adams MD, White O, Clayton RA, Kirkness EF, Kerlavage AR, Bult CJ, Tomb JF, Dougherty BA, Merrick JM, McKenney K, Sutton G, FitzHugh W, Fields CA, Gocaync JD, Scott JD, Shirley R, Liu LI, Glodek A, Kelley JM, Weidman JF, Phillips CA, Spriggs T, Hedblom E, Cotton MD, Utterback TR, Hanna MC, Nguyen DT, Saudek DM, Brandon RC, Fine LD, Fritchman JL, Fuhrmann JL, Geoghagen NSM, Gnehm CL, McDonald LA, Small KV, Fraser CM, Smith HO, Venter JC. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science 269:496-512.
18. Fraser CM, Casjens S, Huang WM, Sutton GG, Clayton RA, Lathigra R, White O, Ketchum KA, Dodson R, Hickey EK, Gwinn M, Dougherty B, Tomb JF, Fleischmann RD, Richardson D, Peterson J, Kerlavage AR, Quackenbush J, Salzberg S, Hanson M, van-Vugt R, Palmer N, Adams MD, Gocayne JD, Weidman J, Utterback T, Watthey L, Mcdonald L, Artiach P, Bowman C, Garland S, Fujii C, Cotton MD, Horst K, Roberts K, Hatch B, Smith HO, Venter JC. 1997. Genomic sequence of a Lyme disease spirochete, Borrelia burgdorferi. Nature 390:580-586.
19. Fraser CM, Gocayne JD, White O, Adams MD, Clayton RA, Fleischmann RD, Bult CJ, Kerlavage AR, Sutton G, Kelley JM, Fritchman JL, Weidman JF, Small KV, Sandusky M, Fuhrmann JL, Nguyen DT, Utterback TR, Saudek DM, Phillips CA, Merrick JM, Tomb JF, Dougherty BA, Bott KF, Hu Pc, Lucier TS, Peterson SN, Smith HO, Hutchison CA III, Venter JC. 1995. The minimal gene complement of Mycoplasma genitalium. Science 270:397-403.
20. Freiberg C, Fellay R, Bairoch A, Broughton WJ, Rosenthal A, Perret X. 1997. Molecular basis of symbiosis between Rhizobium and legumes. Nature 387:394-401.
21. Gase K, Liu G, Bruckmann A, Steiner K, Ozegowski J, Malke H. 1997. The lppC gene of Streptococcus equisimilis encodes a lipoprotein that is homologous to the outer membrane protein e (P4) from Haemophilus influenzae. Med Microbiol Immunol 186:63-73.
22. 2 fixation operon of Rhodobacter sphaeroides. J Biol Chem 266:14646-14653.
23. Green BA, Farley JE, Quinn-Dey T, Deich RA, Zlotnick GW. 1991. The e(P4) outer membrane protein of Haemophilus influenzae: The structural gene. Infect Immun 59:3191-3198.
24. Guerreiro P, Barreiros T, Soares H, Cyrne L, Maia E, Silva A, Rodrigues-Pousada C. 1996. Sequencing of a 176 kb segment on the right arm of yeast chromosome VII reveals 12 ORFs, including CCT, ADE3 and TR-I genes, homologues of the yeast PMT and EF1G genes, of the human and bacterial electron-transferring tlavoproteins (beta-chain) and of the Escherichia coli phosphoserine phosphohydrolase, and five new ORFs. Yeast 12:273-280.
25. Hayashi S, Wu HC. 1990. Lipoproteins in bacteria. J Bioenerg Biomembr 22:451-471.
26. Himmelreich R, Hilbert H, Plagens H, Pirkl E, Li BC, Herrmann R. 1996. Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae. Nucleic Acids Res 24:4420-1449.
27. Kaasen I, McDougall J, Strom AR. 1994. Analysis of the otsBA operon for osmoregulatory trehalose synthesis in Escherichia coli and homology of the OtsA and OtsB proteins to the yeast trehalose-6-phospatase. Gene 145:9-15.
28. Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T,. Watanabe A, Yamada M, Yasuda M, Tabata S. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803 II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109-136.
29. Kasahara M, Nakata A, Shinagawa H. 1991. Molecular analysis of the Salmonella typhimurium phoN gene, which encodes nonspecific acid phosphatase. J Bacterial 173:6770-6775.
30. Klenk HP, Clayton RA, Tomb J, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, Richardson DL, Kerlavage AR, Graham DE, Kyrpides NC, Fleischmann RD, Quackenbush J, Lee NH, Sutton GG, Gill S, Kirkness EF, Dougherty BA, Mckenney K, Adams MD, Loftus B, Peterson S, Reich CI, Mcneil LK, Badger JH, Glodek A, Zhou L, Overbeek R, Gocayne JD, Weidman JF, Mcdonald L, Utterback T, Cotton MD, Spriggs T, Artiach P, Kaine BP, Sykes SM, Sadow PW, D'Andrea KP, Bowman C, Fujii C, Garland SA, Mason TM, Olsen GJ, Fraser CM, Smith HO, Woese CR, Venter JC. 1997. The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 390:364-370
31. Lyngstadaas A, Lobner-Olesen A, Boye E. 1995. Characterization of three genes in the dam-containing operon of Escherichia coli. Mol Gen Genet 247:546-554.
32. Neuwald AF, Stauffer GV. 1985. DNA sequence and characterization of the Escherichia coli serB gene. Nucleic Acids Res 13:7025-7039.
33. Peschke U, Schmidt H, Zhang HZ, Piepersberg W. 1995. Molecular characterization of the lincomycin-production gene cluster of Streptomyces lincolnenxis 78-11. Mol Microbiol 16:1137-1156.
34. + product, from Zymomonas mobilis. J Bacteriol 171:767-774.
35. Schaeferjohann J, Yoo JG, Kusian B, Bowien B. 1993. The cbb operons of the facultative chemoautotroph Alcaligenes eutrophus encode phosphoglycolate phosphatase. J Bacteriol 175:7329-7340.
36. Sensen CW, Klenk HP, Singh RK, Allard G, Chan CC, Liu QY, Penny SL, Young F, Schenk ME, Gaasterland T, Doolittle WF, Ragan MA, Charlebois RL. 1996. Organizational characteristics and information content of an archaeal genome: 156 kb of sequence from Sulfolobus solfataricus P2. Mol Microbiol 22:175-191.
37. Smith DR, Doucette-Stamm LA, Deloughery C, Lee HM, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicare R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Safer H, Patwell D, Prabhakar S, McDougall S, Shimer G, Goyal A, Pietrovski S, Church GM, Daniels CJ, Mao JI, Rice P, Nolling J, Reeve JN. 1997. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: Functional analysis and comparative genomics. J Bacteriol 179:7135-7155.
38. Stukey J, Carman GM. 1997. Identification of a novel phosphatase sequence motif. Protein Sci 6:469-472.
39. Thaller MC, Berlutti F, Schippa S, Iori P, Passariello C, Rossolini GM. 1995a. Heterogeneous patterns of acid phosphatases containing low molecular mass polypeptides in members of the family Enterobacteriaceae. Int J Syst Bacteriol 45:255-261.
40. Thaller MC, Berlutti F, Schippa S, Lombardi G, Rossolini GM. 1994. Characterization and sequence of PhoC, the principal phosphate-irrepressible acid phosphatase of Morganella morganii. Microbiology 140:1341-1350.
41. Thaller MC, Lombardi G, Berlutti F, Schippa S, Rossolini GM. 1995b. Cloning and characterization of the NapA acid phosphatase/phosphotransferase of Morganella morganii: Identification of a new family of bacterial acid phosphatase-encoding genes. Microbiology 141:147-154.
42. Thaller MC, Schippa S, Bonci A, Cresti S, Rossolini GM. 1997a. Identification of the gene (aphA) encoding the class B acid phosphatase/phosphotransferase of Escherichia coli MG1655 and characterization of its product. FEMS Microbiol Lett 146:191-198.
43. Thaller MC, Schippa S, Iori P, Berlutti F, Rossolini GM. 1997b. Cloning of Chryseobacterium meningosepticum acid phosphatase-encoding gene: Identification of a family of outer membrane bacterial phosphatases. Abs 97th General Meeting of the American Society for Microbiology, Miami Beach, Florida, 4-8 May 1997. p 286.
44. Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Hickey EK, Berg DE, Gocayne JD, Utterback TR, Peterson JD, Kelley JM, Cotton MD, Weidman JM, Fujii C, Bowman C, Watthey L, Wallin E, Hayes WS, Borodovsky M, Karp PD, Smith HO, Fraser CM, Venter JC. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
45. Uchiya K, Tohsuji M, Nikai T, Sugihara H, Sasakawa C. 1996. Identification and characterization of phoN-Sf, a gene on the large plasmid of Shigella flexneri 2a encoding a nonspecific phosphatase. J Bacteriol 178:4548-4554.
46. Uerkvitz W. 1988. Periplasmic nonspecific phosphatase II from Salmonella typhimurium LT2. J Biol Chem 263:15823-15830.
47. Walkenhorst HM, Hemschemeier SK, Eichenlaub R. 1995. Molecular analysis of the molybdate uptake operon, modABCD, of Escherichia coli and modR, a regulatory gene. Microbiol Res 150:347-361.
48. Yamane K, Kumano M, Kurita K. 1996. The 25 degrees-36 degrees region of the Bacillus subtilis chromosome: Determination of the sequence of a 146 kb segment and identification of 113 genes. Microbiology 142:3047-3056.
49. Yoshida K, Fujimura M, Yanai N, Fujita Y. 1995. Cloning and sequencing of a 23-kb region of the Bacillus subtilis genome between the iol and hut operons. DNA Res 2:295-301.