Transcriptomic changes arising during light-induced sporulation in Physarum polycephalum

BMC Genomics

Volumn 11, Issue 1, 2010, Pages

  Barrantes, Israel ^a,d   Glockner, Gernot ^b,c,e   Meyer, Sonja ^d   Marwan, Wolfgang ^d  

^a International Max Planck Research School   (Germany)

^b FRITZ LIPMANN INSTITUTE   (Germany)

^c UNIVERSITY OF COLOGNE   (Germany)

^d OTTO VON GUERICKE UNIVERSITY   (Germany)

^e Berlin Center for Genomics in Biodiversity Research Leibniz Institute   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ACTIN BINDING PROTEIN; CALCIUM; COMPLEMENTARY DNA; ACTIN; PROTOZOAL RNA;

AMINO ACID SEQUENCE; ARTICLE; CALCIUM TRANSPORT; CELL DEATH; CELL DIFFERENTIATION; CELL DIVISION; CELL POLARITY; CONTROLLED STUDY; DNA REPAIR; DNA SYNTHESIS; GENE EXPRESSION REGULATION; LIGHT EXPOSURE; MIGRATION INHIBITION; NONHUMAN; ORTHOLOGY; PHYSARUM POLYCEPHALUM; RNA ISOLATION; SIGNAL TRANSDUCTION; SPOROGENESIS; TRANSCRIPTOMICS; DNA SEQUENCE; GENE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; LIGHT; METABOLISM; RADIATION EXPOSURE;

AMOEBOZOA; METAZOA; PHYSARUM; PHYSARUM POLYCEPHALUM; PROTISTA;

ACTINS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE LIBRARY; GENE REGULATORY NETWORKS; GENES, PROTOZOAN; LIGHT; METABOLIC NETWORKS AND PATHWAYS; PHYSARUM POLYCEPHALUM; RNA, PROTOZOAN; SEQUENCE ANALYSIS, DNA;

EID: 77949430100     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-11-115     Document Type: Article

References (83)

1. Burland TG, Solnica-Krezel L, Bailey J, Cunningham DB, Dove WF. Patterns of inheritance development and the mitotic cycle in the protist Physarum polycephalum. Adv Microbial Physiol 1993, 35:1-69.
2. Martel R, Tessier A, Pallotta D, Lemieux G. Selective gene expression during sporulation of Physarum polycephalum. J Bacteriol 1988, 170:4784-4790. 211521, 3170484.
3. Kroneder R, Cashmore AR, Marwan W. Phytochrome-induced expression of lig1 a homologue of the fission yeast cell-cycle checkpoint gene hus1 is associated with the developmental switch in Physarum polycephalum plasmodia. Curr Genet 1999, 36:86-93.
4. Golderer G, Werner ER, Leitner S, Grobner P, Werner-Felmayer G. Nitric oxide synthase is induced in sporulation of Physarum polycephalum. Genes Dev 2001, 15:1299-1309. 313797, 11358872.
5. Watkins RF, Gray MW. Sampling gene diversity across the supergroup amoebozoa: Large EST data sets from Acanthamoeba castellanii, Hartmannella vermiformis, Physarum polycephalum, Hyperamoeba dachnaya and Hyperamoeba sp. Protist 2008, 159:269-281.
6. Glockner G, Golderer G, Werner-Felmayer G, Meyer S, Marwan W. A first glimpse at the transcriptome of Physarum polycephalum. BMC Genomics 2008, 9:6. 2258281, 18179708.
7. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim JB, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-80. 1464427, 16056220.
8. Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nature Rev Genet 2009, 10:57-63.
9. Audic S, Claverie JM. The significance of digital gene expression profiles. Genome Res 1997, 7(10):986-95.
10. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2008, 36:D25-30. 2238942, 18073190.
11. 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. 146917, 9254694.
12. Boeckmann B, Bairoch A, Apweiler R, Blatter MC, Estreicher A, Gasteiger E, Martin MJ, Michoud K, O'Donovan C, Phan I, Pilbout S, Schneider M. The Swiss-Prot protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res 2003, 31:365-370. 165542, 12520024.
13. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes transcripts and proteins. Nucleic Acids Res 2007, 35:D61-5. 1716718, 17130148.
14. Chisholm RL, Gaudet P, Just EM, Pilcher KE, Fey P, Merchant SN, Kibbe WA. dictybase, the model organism database for Dictyostelium discoideum. Nucleic Acids Res 2006, 34:D423-7. 1347453, 16381903.
15. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: A tool for the unification of biology. Nature Genet 2000, 25:25-29.
16. Gotz S, Garcia-Gomez JM, Terol J, Williams TD, Nagaraj SH, Nueda MJ, Robles M, Talon M, Dopazo J, Conesa A. High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res 2008, 36(10):3420-35. 2425479, 18445632.
17. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, et al. Interpro: the integrative protein signature database. Nucleic Acids Res 2009, 37:D211-5. 2686546, 18940856.
18. Bluthgen N, Brand K, Cajavec B, Swat M, Herzel H, Beule D. Biological profiling of gene groups utilizing gene ontology. Genome Informat 2005, 16:106-115.
19. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-4. 2238879, 18077471.
20. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res 2007, 35:W182-5. 1933193, 17526522.
21. Okuda S, Yamada T, Hamajima M, Itoh M, Katayama T, Bork P, Goto S, Kanehisa M. KEGG atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res 2008, 36:W423-6. 2447737, 18477636.
22. Ge H, Liu Z, Church GM, Vidal M. Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae. Nature Genet 2001, 29:482-486.
23. Fraser HB, Hirsh AE, Wall DP, Eisen MB. Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci USA 2004, 101:9033-9038. 439012, 15175431.
24. Morcos F, Lamanna C, Sikora M, Izaguirre J. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. Bioinformatics 2008, 24(19):2265-6.
25. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res 2003, 13(11):2498-504. 403769, 14597658.
26. Deng M, Mehta S, Sun F, Chen T. Inferring domain-domain interactions from protein-protein interactions. Genome Res 2002, 12(10):1540-8. 187530, 12368246.
27. Bailey J. Building a plasmodium: Development in the acellular slime mould Physarum polycephalum. Bio Essays 1997, 19:985-992.
28. Bailey J, Cook LJ, Kilmer-Barber R, Swanston E, Solnica-Krezel L, Lohman K, Dove WF, Dee J, Anderson RW. Identification of three genes expressed primarily during development in Physarum polycephalum. Arch Microbiol 1999, 172:364-376.
29. Shirai Y, Sasaki N, Kishi Y, Izumi A, Itoh K, Sameshima M, Kobayashi T, Murakami-Murofushi K. Regulation of levels of actin threonine phosphorylation during life cycle of Physarum polycephalum. Cell Motil Cytoskel 2006, 63:77-87.
30. Binette F, Benard M, Laroche A, Pierron G, Lemieux G, Pallotta D. Cell-specific expression of a profilin gene family. DNA Cell Biol 1990, 9:323-334.
31. de Hostos EL, Bradtke B, Lottspeich F, Gerisch G. Coactosin, a 17 kda f-actin binding protein from Dictyostelium discoideum. Cell Motil Cytoskel 1993, 26:181-191.
32. Vandekerckhove J, Van Damme J, Vancompernolle K, Bubb MR, Lambooy PK, Korn ED. The covalent structure of Acanthamoeba actobindin. J Biol Chem 1990, 265:12801-12805.
33. Rohrig U, Gerisch G, Morozova L, Schleicher M, Wegner A. Coactosin interferes with the capping of actin filaments. FEBS Lett 1995, 374:284-286.
34. Brulle F, Cocquerelle C, Mitta G, Castric V, Douay F, Lepretre A, Vandenbulcke F. Identification and expression profile of gene transcripts differentially expressed during metallic exposure in Eisenia fetida coelomocytes. Dev Comp Immunol 2008, 32:1441-1453.
35. Khaire N, Muller R, Blau-Wasser R, Eichinger L, Schleicher M, Rief M, Holak TA, Noegel AA. Filamin-regulated f-actin assembly is essential for morphogenesis and controls phototaxis in Dictyostelium. J Biol Chem 2007, 282:1948-1955.
36. T'Jampens D, Bailey J, Cook LJ, Constantin B, Vandekerckhove J, Gettemans J. Physarum amoebae express a distinct fragmin-like actin-binding protein that controls in vitro phosphorylation of actin by the actin- fragmin kinase. Eur J Biochem 1999, 265:240-250.
37. Howe A. Regulation of actin-based cell migration by cAMP/PKA. Biochim Biophys Acta 2004, 1692(2-3):159-174.
38. Aubry L, Firtel R. Integration of signaling networks that regulate Dictyostelium differentiation. Ann Rev Cell Dev Biol 1999, 15:469-517.
39. Stettler S, Warbrick E, Prochnik S, Mackie S, Fantes P. The wis1 signal transduction pathway is required for expression of cAMP-repressed genes in fission yeast. J Cell Sci 1996, 109:1927-1935.
40. Fujioka H, Shimoda C. A mating-type-specific sterility gene map1 is required for transcription of a mating-type gene mat1-Pi in the fission yeast Schizosaccharomyces pombe. FEMS Microbiol Lett 1989, 51(1):45-8.
41. Christmann M, Tomicic MT, Origer J, Kaina B. Fen1 is induced p53 dependently and involved in the recovery from uv-light-induced replication inhibition. Oncogene 2005, 24:8304-8313.
42. Larsen E, Kleppa L, Meza TJ, Meza-Zepeda LA, Rada C, Castellanos CG, Lien GF, Nesse GJ, Neuberger MS, Laerdahl JK, William Doughty R, Klungland A. Early-onset lymphoma and extensive embryonic apoptosis in two domain-specific FEN1 mice mutants. Cancer Res 2008, 68:4571-4579.
43. Cerutti L, Simanis V. Asymmetry of the spindle pole bodies and spg1p gap segregation during mitosis in fission yeast. J Cell Sci 1999, 112:2313-2321.
44. Fankhauser C, Marks J, Reymond A, Simanis V. The S. pombe cdc16 gene is required both for maintenance of p34cdc2 kinase activity and regulation of septum formation: a link between mitosis and cytokinesis?. EMBO J 1993, 12:2697-2704. 413518, 8334988.
45. Lin H, Spradling AC. A novel group of pumilio mutations affects the asymmetric division of germline stem cells in the Drosophila ovary. Development 1997, 124(12):2463-76.
46. Jin J, Cardozo T, Lovering RC, Elledge SJ, Pagano M, Harper JW. Systematic analysis and nomenclature of mammalian F-box proteins. Genes Dev 2004, 18:2573-2580. 525538, 15520277.
47. Meijer HJ, Latijnhouwers M, Ligterink W, Govers F. A transmembrane phospholipase D in Phytophthora; a novel PLD subfamily. Gene 2005, 350:173-182.
48. Yu LP, Miller AK, Clark SE. Poltergeist encodes a protein phosphatase 2c that regulates clavata pathways controlling stem cell identity at Arabidopsis shoot and flower meristems. Curr Biol 2003, 13:179-188.
49. Iwasaki W, Sasaki H, Nakamura A, Kohama K, Tanokura M. Crystallization and preliminary x-ray diffraction studies of a 40 kda calcium binding protein specifically expressed in plasmodia of Physarum polycephalum. J Biochem 1999, 126:7-9.
50. Mottahedeh J, Marsh R. Characterization of 101-kda transglutaminase from Physarum polycephalum and identification of LAV1-2 as substrate. J Biol Chem 1998, 273:29888-29895.
51. Yap KL, Yuan T, Mal TK, Vogel HJ, Ikura M. Structural basis for simultaneous binding of two carboxy-terminal peptides of plant glutamate decarboxylase to calmodulin. J Mol Biol 2003, 328:193-204.
52. Schlatterer C, Gollnick F, Schmidt E, Meyer R, Knoll G. Challenge with high concentrations of cyclic AMP induces transient changes in the cytosolic free calcium concentration in Dictyostelium discoideum. J Cell Sci 1994, 107:2107-2115.
53. Renzel S, Esselborn S, Sauer HW, Hildebrandt A. Calcium and Malate Are Sporulation-Promoting Factors of Physarum polycephalum. J Bacteriol 2000, 182(24):6900-6905. 94813, 11092848.
54. Furukawa R, Maselli A, Thomson SAM, Lim RWL, Stokes JV, Fechheimer M. Calcium regulation of actin crosslinking is important for function of the actin cytoskeleton in Dictyostelium. J Cell Sci 2003, 116:187-196.
55. Moniakis J, Coukell MB, Janiec A. Involvement of the Ca2+-ATPase PAT1 and the contractile vacuole in calcium regulation in Dictyostelium discoideum. J Cell Sci 1999, 112:405-414.
56. Quinlan ME, Heuser JE, Kerkhoff E, Mullins DD. Drosophila spire is an actin nucleation factor. Nature 2005, 433:382-388.
57. Blanchoin L, Robinson RC, Choe S, Pollard TD. Phosphorylation of Acanthamoeba actophorin (ADF/cofilin) blocks interaction with actin without a change in atomic structure. J Mol Biol 2000, 295(2):203-11.
58. Yang F, Demma M, Warren V, Dharmawardhane S, Condeelis J. Identification of an actin- binding protein from Dictyostelium as elongation factor 1a. Nature 1990, 347:494-496.
59. Edmonds BT, Bell A, Wyckoff J, Condeelis J, Leyh TS. The effect of F-actin on the binding and hydrolysis of guanine nucleotide by Dictyostelium elongation factor 1A. J Biol Chem 1998, 273(17):10288-95.
60. Gross SR, Kinzy TG. Improper organization of the actin cytoskeleton affects protein synthesis at initiation. Mol Cell Biol 2007, 27:1974-1989. 1820457, 17178834.
61. Munshi R, Kandl KA, Carr-Schmid A, Whitacre JL, Adams AE, Kinzy TG. Overexpression of translation elongation factor 1a affects the organization and function of the actin cytoskeleton in yeast. Genetics 2001, 157:1425-1436. 1461591, 11290701.
62. Bluem R, Schmidt E, Corvey C, Karas M, Schlicksupp A, Kirsch J, Kuhse J. Components of the translational machinery are associated with juvenile glycine receptors and are redistributed to the cytoskeleton upon aging and synaptic activity. J Biol Chem 2007, 282:37783-37793.
63. Jeganathan S, Morrow A, Amiri A, Lee JM. Eukaryotic elongation factor 1a2 cooperates with phosphatidylinositol-4 kinase III beta to stimulate production of filopodia through increased phosphatidylinositol-45 bisphosphate generation. Mol Cell Biol 2008, 28:4549-4561. 2447124, 18474610.
64. Li P, Maines-Bandiera S, Kuo WL, Guan Y, Sun Y, Hills M, Huang G, Collins CC, Leung PC, Gray JW, Auersperg N. Multiple roles of the candidate oncogene ZNF217 in ovarian epithelial neoplastic progression. Int J Cancer 2007, 120(9):1863-73.
65. Datta S, Firtel RA. Identification of the sequences controlling cyclic AMP regulation and cell-type-specific expression of a prestalk-specific gene in Dictyostelium discoideum. Mol Cell Biol 1987, 7:149-159. 365051, 3031453.
66. Pope SN, Lee IR. Yeast two-hybrid identification of prostatic proteins interacting with human sex hormone-binding globulin. J Steroid Biochem Mol Biol 2005, 94(1-3):203-8.
67. Fukuzawa M, Williams JG. Analysis of the promoter of the cudA gene reveals novel mechanisms of Dictyostelium cell type differentiation. Development 2000, 127:2705-2713.
68. Yamada Y, Wang HY, Fukuzawa M, Barton GJ, Williams JG. A new family of transcription factors. Development 2008, 135(18):3093-101.
69. Li P, Maines-Bandiera S, Kuo WL, Guan Y, Sun Y, Hills M, Huang G, Collins CC, Leung PC, Gray JW, Auersperg N. Multiple roles of the candidate oncogene ZNF217 in ovarian epithelial neoplastic progression. Int J Cancer 2007, 120:1863-1873.
70. Gualtieri T, Ragni E, Mizzi L, Fascio U, Popolo L. The cell wall sensor wsc1p is involved in reorganization of actin cytoskeleton in response to hypo-osmotic shock in Saccharomyces cerevisiae. Yeast 2004, 21:1107-1120.
71. Serrano R, Martin H, Casamayor A, Arino J. Signaling alkaline pH stress in the yeast Saccharomyces cerevisiae through the WSC1 cell surface sensor and the SLT2 MAPK pathway. J Biol Chem 2006, 281(52):39785-95.
72. Delley PA, Hall MN. Cell wall stress depolarizes cell growth via hyperactivation of RHO1. J Cell Biol 1999, 147(1):163-74. 2164985, 10508863.
73. Cerutti L, Simanis V. Asymmetry of the spindle pole bodies and spg1p gap segregation during mitosis in fission yeast. J Cell Sci 1999, 112:2313-2321.
74. Chung CY, Firtel RA. PakA, a putative pak family member, is required for cytokinesis and the regulation of the cytoskeleton in Dictyostelium discoideum cells during chemotaxis. J Cell Biol 1999, 147:559-576. 2151188, 10545500.
75. Pathak R, Bogomolnaya LM, Guo J, Polymenis M. Gid8p (dcr1p) and dcr2p function in a common pathway to promote start completion in Saccharomyces cerevisiae. Eukaryotic Cell 2004, 3:1627-1638. 539013, 15590836.
76. Miles RR, Sluka JP, Santerre RF, Hale LV, Bloem L, Boguslawski G, Thirunavukkarasu K, Hock JM, Onyia JE. Dynamic regulation of RGS2 in bone: Potential new insights into parathyroid hormone signaling mechanisms. Endocrinology 2000, 141:28-36.
77. Seibenhener ML, Geetha T, Wooten MW. Sequestosome 1/p62 - More than just a scaffold. FEBS Lett 2007, 581(2):175-179. 1850379, 17188686.
78. Bjorkoy G, Lamark T, Brech A, Outzen H, Perander M, Overvatn A, Stenmark H, Johansen T. p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death. J Cell Biol 2005, 171(4):603-14. 2171557, 16286508.
79. Puls A, Schmidt S, Grawe F, Stabel S. Interaction of Protein Kinase C zeta with ZIP, a novel Protein Kinase C- binding protein. Proc Natl Acad Sci USA 1997, 94:6191-6196. 21025, 9177193.
80. Tokumoto M, Horiguchi R, Nagahama Y, Ishikawa K, Tokumoto T. Two proteins, a goldfish 20s proteasome subunit and the protein interacting with 26s proteasome, change in the meiotic cell cycle. Eur J Biochem 2000, 267:97-103.
81. Mizuno K, Kitamura A, Sasaki T. Rabring7, a novel rab7 target protein with a ring finger motif. Mol Biol Cell 2003, 14:3741-3752. 196564, 12972561.
82. Rampp M, Soddemann T, Lederer H. The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis. Nucleic Acids Res 2006, 34:W15-9. 1538907, 16844980.
83. Myhre S, Tveit H, Mollestad T, Laegreid A. Additional gene ontology structure for improved biological reasoning. Bioinformatics 2006, 22:2020-2027.