Gene discovery in the Acanthamoeba castellanii genome

Protist

Volumn 156, Issue 2, 2005, Pages 203-214

  Anderson, Iain J ^a,d   Watkins, Russell F ^b   Samuelson, John ^c   Spencer, David F ^b   Majoros, William H ^a   Gray, Michael W ^b   Loftus, Brendan J ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b DALHOUSIE UNIVERSITY   (Canada)

^c BOSTON UNIVERSITY   (United States)

^d DOE JOINT GENOME INSTITUTE   (United States)

Author keywords

Acanthamoeba; Free living amoeba; Genome sequence; Metabolism

Indexed keywords

ACANTHAMOEBA; ACANTHAMOEBA CASTELLANII; DICTYOSTELIUM DISCOIDEUM; ENTAMOEBA HISTOLYTICA; PROTISTA;

EID: 22744458161     PISSN: 14344610     EISSN: 16180941     Source Type: Journal    
DOI: 10.1016/j.protis.2005.04.001     Document Type: Article

References (69)

1. H. Abd, T. Johansson, I. Golovliov, G. Sandström, and M. Forsman Survival and growth of Francisella tularensis in Acanthamoeba castellanii Appl Environ Microbiol 69 2003 600 606
2. A.J. Anderson, and E.A. Dawes Occurrence, metabolism, metabolic role, and industrial uses of bacterial polyhydroxyalkanoates Microbiol Rev 54 1990 450 472
3. A. Aspegren, A. Hinas, P. Larsson, A. Larsson, and F. Söderbom Novel non-coding RNAs in Dictyostelium discoideum and their expression during development Nucleic Acids Res 32 2004 4646 4656
4. S.L. Baldauf, A.J. Roger, I. Wenk-Siefert, and W.F. Doolittle A kingdom-level phylogeny of eukaryotes based on combined protein data Science 290 2000 972 977
5. E. Bapteste, H. Brinkmann, J.A. Lee, D.V. Moore, C.W. Sensen, P. Gordon, L. Duruflé, T. Gaasterland, P. Lopez, M. Müller, and H. Philippe The analysis of 100 genes supports the grouping of three highly divergent amoebae: Dictyostelium, Entamoeba, and Mastigamoeba Proc Natl Acad Sci USA 99 2002 1414 1419
6. J. Barbeau, and T. Buhler Biofilms augment the number of free-living amoebae in dental unit waterlines Res Microbiol 152 2001 753 760
7. A. Bateman, L. Coin, R. Durbin, R.D. Finn, V. Hollich, S. Griffiths-Jones, A. Khanna, M. Marshall, S. Moxon, E.L.L. Sonnhammer, D.J. Studholme, C. Yeats, and S.R. Eddy The Pfam protein families database Nucleic Acids Res 32 2004 D138 D141
8. E. Birney, M. Clamp, and R. Durbin GeneWise and Genomewise Genome Res 14 2004 988 995
9. A. Boyd, and A.M. Chakrabarty Role of alginate lyase in cell detachment of Pseudomonas aeruginosa Appl Environ Microbiol 60 1994 2355 2359
10. M.R.W. Brown, A.W. Smith, J. Barker, T.J. Humphrey, and B. Dixon E. coli O157 persistence in the environment Microbiology 148 2002 1 2
11. T.J. Byers Molecular biology of DNA in Acanthamoeba, Amoeba, Entamoeba, and Naegleria Int Rev Cytol 99 1986 311 341
12. Z. Cao, D.M. Jefferson, and N. Panjwani Role of carbohydrate-mediated adherence in cytopathogenic mechanisms of Acanthamoeba J Biol Chem 273 1998 15838 15845
13. L. Chen, Z. Peng, and E. Bateman In vivo interactions of the Acanthamoeba TBP gene promoter Nucleic Acids Res 32 2004 1251 1260
14. J.D. Cirillo, S. Falkow, L.S. Tompkins, and L.E. Bermudez Interaction of Mycobacterium avium with environmental amoebae enhances virulence Infect Immun 65 1997 3759 3767
15. J.D. Cirillo, S.L.G. Cirillo, L. Yan, L.E. Bermudez, S. Falkow, and L.S. Tompkins Intracellular growth in Acanthamoeba castellanii affects monocyte entry mechanisms and enhances virulence of Legionella pneumophila Infect Immun 67 1999 4427 4434
16. M. Clarholm Bacteria and protozoa as integral components of the forest ecosystem - their role in creating a naturally varied soil fertility Antonie Van Leeuwenhoek 81 2002 309 318
17. J.W. Costerton, Z. Lewandowski, D.E. Caldwell, D.R. Korber, and H.M. Lappin-Scott Microbial biofilms Annu Rev Microbiol 49 1995 711 745
18. A.D. Elbein, Y.T. Pan, I. Pastuszak, and D. Carroll New insights on trehalose: a multifunctional molecule Glycobiology 13 2003 17R 27R
19. A. Essig, M. Heinemann, U. Simnacher, and R. Marre Infection of Acanthamoeba castellanii by Chlamydia pneumoniae Appl Environ Microbiol 63 1997 1396 1399
20. J.F. Fahrni, I. Bolivar, C. Berney, E. Nassonova, A. Smirnov, and J. Pawlowski Phylogeny of lobose amoebae based on actin and small-subunit ribosomal RNA genes Mol Biol Evol 20 2003 1881 1886
21. J. Felsenstein PHYLIP - phylogeny inference package (version 3.2) Cladistics 5 1989 164 166
22. P. Gacesa Bacterial alginate biosynthesis - recent progress and future prospects Microbiology 144 1998 1133 1143
23. M. Garate, Z. Cao, E. Bateman, and N. Panjwani Cloning and characterization of a novel mannose-binding protein of Acanthamoeba J Biol Chem 279 2004 29849 29856
24. M.J. Gardner, S.J. Shallom, J.M. Carlton, S.L. Salzberg, V. Nene, A. Shoaibi, A. Ciecko, J. Lynn, M. Rizzo, B. Weaver, B. Jarrahi, M. Brenner, B. Parvizi, L. Tallon, A. Moazzez, D. Granger, C. Fujii, C. Hansen, J. Pederson, T. Feldblyum, J. Peterson, B. Suh, S. Angiuoli, M. Pertea, J. Allen, J. Selengut, O. White, L.M. Cummings, H.O. Smith, M.D. Adams, J.C. Venter, D.J. Carucci, S.L. Hoffman, and C.M. Fraser Sequence of Plasmodium falciparum chromosomes 2, 10, 11, and 14 Nature 419 2002 531 534
25. W.H. Gaze, N. Burroughs, M.P. Gallagher, and E.M.H. Wellington Interactions between Salmonella typhimurium and Acanthamoeba polyphaga, and observation of a new mode of intracellular growth within contractile vacuoles Microbial Ecol 46 2003 358 369
26. G. Glöckner, L. Eichinger, K. Szafranski, J.A. Pachebat, A.T. Bankier, P.H. Dear, R. Lehmann, C. Baumgart, G. Parra, J.F. Abril, R. Guigó, K. Kumpf, B. Tunggal, E. Cox, M.A. Quail, M. Platzer, A. Rosenthal, A.A. Noegel, B.G. Barrell, M-A. Rajandream, J.G. Williams, R.R. Kay, A. Kuspa, R. Gibbs, R. Sucgang, D. Muzny, B. Desany, K. Zeng, B. Zhu, P. de Jong, T. Dingermann, G. Gerisch, P. Philippsen, M. Schleicher, S.C. Schuster, and T. Winckler Sequence and analysis of chromosome 2 of Dictyostelium discoideum Nature 418 2002 79 85
27. G. Greub, B. La Scola, and D. Raoult Parachlamydia acanthamoeba is endosymbiotic or lytic for Acanthamoeba polyphaga depending on the incubation temperature Ann N Y Acad Sci 990 2003 628 634
28. B.J. Haas, A.L. Delcher, S.M. Mount, J.R. Wortman, R.K. Smith Jr., L.I. Hannick, R. Maiti, C.M. Ronning, D.B. Rusch, C.D. Town, S.L. Salzberg, and O. White Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies Nucleic Acids Res 31 2003 5654 5666
29. M. Hurt, J. Niederkorn, and H. Alizadeh Effects of mannose on Acanthamoeba castellanii proliferation and cytolytic ability to corneal epithelial cells Invest Ophthlmol Vis Sci 44 2003 3424 3431
30. D.H. Huson, K. Reinert, S.A. Kravitz, K.A. Remington, A.L. Delcher, I.M. Dew, M. Flanigan, A.L. Halpern, Z. Lai, C.M. Mobarry, G.G. Sutton, and E.W. Myers Design of a compartmentalized shotgun assembler for the human genome Bioinformatics 17 Suppl 1 2001 S132 S139
31. T.J.J. Inglis, P. Rigby, T.A. Robertson, N.S. Dutton, M. Henderson, and B.J. Chang Interaction between Burkholderia pseudomallei and Acanthamoeba species results in coiling phagocytosis, endamebic bacterial survival, and escape Infect Immun 68 2000 1681 1686
32. T. Jacobs, and M. Leippe Purification and molecular cloning of a major antibacterial protein of the protozoan parasite Entamoeba histolytica with lysozyme-like properties Eur J Biochem 231 1995 831 838
33. N. King, C.T. Hittinger, and S.B. Carroll Evolution of key cell signaling and adhesion protein families predates animal origins Science 301 2003 361 363
34. B. La Scola, and D. Raoult Survival of Coxiella burnetii within free-living amoeba Acanthamoeba castellanii Clin Microbiol Infect 7 2001 75 79
35. B. La Scola, S. Audic, C. Robert, L. Jungang, X. de Lamballerie, M. Drancourt, R. Birtles, J.J.-M. Claverie, and D. Raoult A giant virus in amoebae Science 299 2003 2033
36. M. Leippe, J. Andra, R. Nickel, E. Tannich, and H.J. Muller-Eberhard Amoebapores, a family of membranolytic peptides from cytoplasmic granules of Entamoeba histolytica: isolation, primary structure, and pore formation in bacterial cytoplasmic membranes Mol Microbiol 14 1994 895 904
37. B. Loftus, I. Anderson, R. Davies, U.C.M. Alsmark, J. Samuelson, P. Amedeo, P. Roncaglia, M. Berriman, R.P. Hirt, B.J. Mann, T. Nozaki, B. Suh, M. Pop, M. Duchene, J. Ackers, E. Tannich, M. Leippe, M. Hofer, I. Bruchhaus, U. Willhoeft, A. Bhattacharya, T. Chillingworth, C. Churcher, Z. Hance, B. Harris, D. Harris, K. Jagels, S. Moule, K. Mungall, D. Ormond, R. Squares, S. Whitehead, M.A. Qualil, E. Rabbinowitsch, H. Norbertczak, C. Price, Z. Wang, N. Guillén, C. Gilchrist, S.E. Stroup, S. Bhattacharya, A. Lohia, P.G. Foster, T. Sicheritz-Ponten, C. Weber, U. Singh, C. Mukherjee, N.M. El-Sayed, WA. Petri Jr., C.G. Clark, T.M. Embley, B. Barrell, C.M. Fraser, and N. Hall The genome of the protist parasite Entamoeba histolytica Nature 433 2005 865 868
38. T.M. Lowe, and S.R. Eddy tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence Nucleic Acids Res 25 1997 955 964
39. T.M. Lowe, and S.R. Eddy A computational screen for methylation guide snoRNAs in yeast Science 283 1999 1168 1171
40. R.M. MacKay, and W.F. Doolittle Nucleotide sequences of Acanthamoeba castellanii 5S and 5.8S ribosomal ribonucleic acids: phylogenetic and comparative structural analyses Nucleic Acids Res 9 1981 3321 3334
41. W.H. Majoros, M. Pertea, and S.L. Salzberg TigrScan and GlimmerHMM: two open-source ab initio eukaryotic gene-finders Bioinformatics 20 2004 2878 2879
42. H. Maki, A. Mori, K. Fujiyama, S. Kinoshita, and T. Yoshida Cloning, sequence analysis, and expression in Escherichia coli of a gene encoding an alginate lyase from Pseudomonas sp. OS-ALG-9 J Gen Microbiol 139 1993 987 993
43. F. Marciano-Cabral, and G. Cabral Acanthamoeba spp. as agents of disease in humans Clin Microbiol Rev 16 2003 273 307
44. M.M. Marshall, D. Naumovitz, Y. Ortega, and C.R. Sterling Waterborne protozoan pathogens Clin Microbiol Rev 10 1997 67 85
45. V. Mermall, P.L. Post, and M.S. Mooseker Unconventional myosins in cell movement, membrane traffic, and signal transduction Science 279 1998 527 533
46. R. Michel, K.-D. Müller, and R. Hoffmann Enlarged Chlamydia-like organisms as spontaneous infection of Acanthamoeba castellanii Parasitol Res 87 2001 248 251
47. E.C. Miltner, and L.E. Bermudez Mycobacterium avium grown in Acanthamoeba castellanii is protected from the effects of antimicrobials Antimicrob Agents Chemother 44 2000 1990 1994
48. D. Moncada, K. Keller, and K. Chadee Entamoeba histolytica cysteine proteinases disrupt the polymeric structure of colonic mucin and alter its protective function Infect Immun 71 2003 838 844
49. R.J. Neff, S.A. Ray, W.F. Benton, and M. Wilborn Induction of Synchronous Encystment (Differentiation) in Acanthamoeba sp D.M. Prescott Methods in Cell Physiology Vol. 1 1964 Academic Press New York 55 83
50. X. Que, and S.L. Reed Cysteine proteinases and the pathogenesis of amebiasis Clin Microbiol Rev 13 2000 196 206
51. R. Rodríguez-Zaragoza Ecology of free-living amoebae Crit Rev Microbiol 20 1994 225 241
52. R. Roth, and M. Sussman Trehalose synthesis in the cellular slime mold Dictyostelium discoideum Biochim Biophys Acta 122 1966 225 231
53. H.A. Schmidt,, K. Strimmer,, M. Vingron,, and A. von Haeseler, TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing Bioinformatics 18 2002 502 504
54. F.L. Schuster, Cultivation of pathogenic and opportunistic free-living amebas Clin Microbiol Rev 15 2002 342 354
55. G. Segal, and H.A. Shuman Legionella pneumophila utilizes the same genes to multiply within Acanthamoeba castellanii and human macrophages Infect Immun 67 1999 2117 2124
56. P.J. Senior, and E.A. Dawes The regulation of poly beta-hydroxybutyrate metabolism in Azotobacter beijerinckii Biochem J 134 1973 225 238
57. P.A. Simmons, A. Tomlinson, and D.V. Seal The role of Pseudomonas aeruginosa biofilm in the attachment of Acanthamoeba to four types of hydrogel contact lens materials Optom Vis Sci 75 1998 860 866
58. F.E. Sluse, and W. Jarmuszkiewicz Uncoupling proteins outside the animal and plant kingdoms: functional and evolutionary aspects FEBS Lett 510 2002 117 120
59. J.N. Steenbergen, H.A. Shuman, and A. Casadevall Cryptococcus neoformans interactions with amoebae suggest an explanation for its virulence and intracellular pathogenic strategy in macrophages Proc Natl Acad Sci USA 98 2001 15245 15250
60. B.L. Taylor, and I.B. Zhulin PAS domains: internal sensors of oxygen, redox potential, and light Microbiol Mol Biol Rev 63 1999 479 506
61. P. Thomason, and R. Kay Eukaryotic signal transduction via histidine-aspartate phosphorelay J Cell Sci 113 2000 3141 3150
62. A.J. Turner, C.D. Brown, J.A. Carson, and K. Barnes The neprilysin family in health and disease Adv Exp Med Biol 477 2000 229 240
63. P.V. Vignais The superoxide-generating NADPH oxidase: structural aspects and activation mechanism Cell Mol Life Sci 59 2002 1428 1459
64. R.A. Weisman Differentiation in Acanthamoeba castellanii Annu Rev Microbiol 30 1976 189 219
65. J. Winiecka-Krusnell, K. Wreiber, A. von Euler, L. Engstrand, and E. Linder Free-living amoebae promote growth and survival of Helicobacter pylori Scand J Infect Dis 344 2002 253 256
66. J.M. Wong, F. Liu, and E. Bateman Isolation of genomic DNA encoding transcription factor TFIID from Acanthamoeba castellanii: characterization of the promoter Nucleic Acids Res 20 1992 4817 4824
67. T.Y. Wong, L.A. Preston, and N.L. Schiller Alginate lyase: review of major sources and enzyme characteristics, structure-function analysis, biological roles, and applications Annu Rev Microbiol 54 2000 289 340
68. Z. Zhang, L. Yan, L. Wang, K.B. Seydel, E. Li, S. Ankri, D. Mirelman, and S.L. Stanley Jr Entamoeba histolytica cysteine proteinases with interleukin-1 beta converting enzyme (ICE) activity cause intestinal inflammation and tissue damage in amoebiasis Mol Microbiol 37 2000 542 548
69. M.G. Zwick, M. Wiggs, and M.R. Paule Sequence and organization of 5S RNA genes from the eukaryotic protist Acanthamoeba castellanii Gene 15 1991 153 157