Targeting Fungal Genes by Diced siRNAs: A Rapid Tool to Decipher Gene Function in Aspergillus nidulans

PLoS ONE

Volumn 8, Issue 10, 2013, Pages

  Kalleda, Natarajaswamy ^a   Naorem, Aruna ^a   Manchikatla, Rajam V ^a  

^a UNIVERSITY OF DELHI   (India)

Author keywords

[No Author keywords available]

Indexed keywords

RIBONUCLEASE; SMALL INTERFERING RNA;

ARTICLE; ASPERGILLUS NIDULANS; CONTROLLED STUDY; DOWN REGULATION; FUNGAL GENE; FUNGUS HYPHAE; GENE EXPRESSION; GENE FUNCTION; GENE SEQUENCE; GENE SILENCING; GENE TARGETING; GENETIC TRANSFORMATION; GFP GENE; MULTIGENE FAMILY; NONHUMAN; RASA GENE; RASB GENE; REPORTER GENE; RHIZOBIUM RADIOBACTER; RNA INTERFERENCE;

AGROBACTERIUM TUMEFACIENS; ASPERGILLUS NIDULANS; FUNGAL PROTEINS; RNA INTERFERENCE; RNA, SMALL INTERFERING;

EID: 84885403283     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075443     Document Type: Article

References (55)

1. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, et al. (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806-811.
2. Hamilton AJ, Baulcombe DC, (1999) A species of small antisense RNA in posttranscriptional gene silencing in plants. Science 286: 950-952.
3. Chang SS, Zhang Z, Liu Y, (2012) RNA interference pathways in fungi: mechanisms and functions. Annu Rev Microbiol 66: 305-323.
4. Kim VN, (2003) RNA interference in functional genomics and medicine. J Korean Med Sci 18: 309-318.
5. Devi GR, (2006) siRNA-based approaches in cancer therapy. Cancer Gene Ther 13: 819-829.
6. Gomase VS, Tagore S, (2008) RNAi-a tool for target finding in new drug development. Curr Drug Metab 9: 241-244.
7. Castanotto D, Rossi JJ, (2009) The promises and pitfalls of RNA-interference-based therapeutics. Nature 457: 426-433.
8. Phalon C, Rao DD, Nemunaitis J, (2010) Potential use of RNA interference in cancer therapy. Expert Rev Mol Med 12: e26.
9. Stark GR, Kerr IM, Williums BRG, Silverman RH, Schreiber RD, (1998) How cells respond to interferons. Annu Rev Biochem 67: 227-264.
10. Elbashir SM, Harborth J, Lendeckel W, Yalcin A, Weber K, et al. (2001) Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells. Nature 411: 494-498.
11. Romano N, Macino G, (1992) Quelling: transient inactivation of gene expression in Neurospora crassa by transformation with homologous sequences. Mol Microbiol 6: 3343-3353.
12. Salame TM, Ziv C, Hadar Y, Yarden O, (2011) RNAi as a potential tool for biotechnological applications in fungi. Applied Microbiology and Biotechnology 89: 501-512.
13. Osmani SA, Mirabito PM, (2004) The early impact of genetics on our understanding of cell cycle regulation in Aspergillus nidulans. Fungal Genetics and Biology 41: 401-410.
14. Henriet SSV, Verweij PE, Warris A, (2012) Aspergillus nidulans and chronic granulomatous disease: A unique host-pathogen interaction. Journal of Infectious Diseases 206: 1128-1137.
15. Hammond TM, Bok JW, Andrewski MD, Reyes-Dominguez Y, Scazzocchio C, et al. (2008) RNA silencing gene truncation in the filamentous fungus Aspergillus nidulans. Eukaryot Cell 7: 339-349.
16. Hammond TM, Keller NP, (2005) RNA silencing in Aspergillus nidulans is independent of RNA-dependent RNA polymerases. Genetics 169: 607-617.
17. Khatri M, Rajam MV, (2007) Targeting polyamines of Aspergillus nidulans by siRNA specific to fungal ornithine decarboxylase gene. Med Mycol 45: 211-220.
18. Krappmann S, (2006) Tools to study molecular mechanisms of Aspergillus pathogenicity. Trends in Microbiology 14: 356-364.
19. Schumann U, Ayliffe M, Kazan K, Wang MB, (2010) RNA silencing in fungi. Front Biol 5: 478-494.
20. Caribe dos Santos AC, Sena JA, Santos SC, Dias CV, Pirovani CP, et al. (2009) dsRNA-induced gene silencing in Moniliophthora perniciosa, the causal agent of witches' broom disease of cacao. Fungal Genet Biol 46: 825-836.
21. Holen T, Amarzguioui M, Wiiger MT, Babaie E, Prydz H, (2002) Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor. Nucleic Acids Res 30: 1757-1766.
22. Pei Y, Tuschl T, (2006) On the art of identifying effective and specific siRNAs. Nat Methods 3: 670-676.
23. Shao MX, Nadel JA, (2005) Dual oxidase 1-dependent MUC5AC mucin expression in cultured human airway epithelial cells. Proc Natl Acad Sci U S A 102: 767-772.
24. Jackson AL, Bartz SR, Schelter J, Kobayashi SV, Burchard J, et al. (2003) Expression profiling reveals off-target gene regulation by RNAi. Nat Biotechnol 21: 635-637.
25. Semizarov D, Kroeger P, Fesik S, (2004) siRNA-mediated gene silencing: a global genome view. Nucleic Acids Res 32: 3836-3845.
26. Persengiev SP, Zhu X, Green MR, (2004) Non-specific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs). RNA 10: 12-18.
27. Fedorov Y, Anderson EM, Birmingham A, Reynolds A, Karpilow J, et al. (2006) Off-target effects by siRNA can induce toxic phenotype. RNA 12: 1188-1196.
28. Myers JW, Jones JT, Meyer T, Ferrell JE Jr, (2003) Recombinant dicer efficiently converts large dsRNAs into siRNAs suitable for gene silencing. Nat Biotechnol 21: 324-328.
29. Yang D, Buchholz F, Huang Z, Goga A, Chen CY, et al. (2002) Short RNA duplexes produced by hydrolysis with Escherichia coli RNase III mediate effective RNA interference in mammalian cells. Proc Natl Acad Sci U S A 99: 9942-9947.
30. Morlighem JE, Petit C, Tzertzinis G (2007) Determination of silencing potency of synthetic and RNase III-generated siRNA using a secreted luciferase assay. Biotechniques 42: 599-600, 602, 604-596.
31. Semizarov D, Frost L, Sarthy A, Kroeger P, Halbert DN, et al. (2003) Specificity of short interfering RNA determined through gene expression signatures. Proc Natl Acad Sci U S A 100: 6347-6352.
32. Sheen J, Hwang S, Niwa Y, Kobayashi H, Galbraith DW, (1995) Green-fluorescent protein as a new vital marker in plant cells. Plant J 8: 777-784.
33. Heim R, Cubitt AB, Tsien RY, (1995) Improved green fluorescence. Nature 373: 663-664.
34. Sugui JA, Chang YC, Kwon-Chung KJ, (2005) Agrobacterium tumefaciens-mediated transformation of Aspergillus fumigatus: an efficient tool for insertional mutagenesis and targeted gene disruption. Appl Environ Microbiol 71: 1798-1802.
35. Yuan B, Latek R, Hossbach M, Tuschl T, Lewitter F, (2004) siRNA Selection Server: an automated siRNA oligonucleotide prediction server. Nucleic Acids Res 32: W130-134.
36. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, et al. (2004) Rational siRNA design for RNA interference. Nat Biotechnol 22: 326-330.
37. Som T, Kolaparthi VS, (1994) Developmental decisions in Aspergillus nidulans are modulated by Ras activity. Mol Cell Biol 14: 5333-5348.
38. Fortwendel JR, Panepinto JC, Seitz AE, Askew DS, Rhodes JC, (2004) Aspergillus fumigatus rasA and rasB regulate the timing and morphology of asexual development. Fungal Genet Biol 41: 129-139.
39. Fortwendel JR, Zhao W, Bhabhra R, Park S, Perlin DS, et al. (2005) A fungus-specific ras homolog contributes to the hyphal growth and virulence of Aspergillus fumigatus. Eukaryot Cell 4: 1982-1989.
40. Kadotani N, Nakayashiki H, Tosa Y, Mayama S, (2003) RNA silencing in the phytopathogenic fungus Magnaporthe oryzae. Mol Plant Microbe Interact 16: 769-776.
41. Jochl C, Loh E, Ploner A, Haas H, Huttenhofer A, (2009) Development-dependent scavenging of nucleic acids in the filamentous fungus Aspergillus fumigatus. RNA Biol 6: 179-186.
42. Michielse CB, Hooykaas PJ, van den Hondel CA, Ram AF, (2008) Agrobacterium-mediated transformation of the filamentous fungus Aspergillus awamori. Nat Protoc 3: 1671-1678.
43. Mullins ED, Chen X, Romaine P, Raina R, Geiser DM, et al. (2001) Agrobacterium-mediated transformation of Fusarium oxysporum: An efficient tool for insertional mutagenesis and gene transfer. Phytopathology 91: 173-180.
44. Castanotto D, Sakurai K, Lingeman R, Li H, Shively L, et al. (2007) Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC. Nucleic Acids Res 35: 5154-5164.
45. Tafer H, Ameres SL, Obernosterer G, Gebeshuber CA, Schroeder R, et al. (2008) The impact of target site accessibility on the design of effective siRNAs. Nat Biotechnol 26: 578-583.
46. Koller E, Propp S, Murray H, Lima W, Bhat B, et al. (2006) Competition for RISC binding predicts in vitro potency of siRNA. Nucleic Acids Res 34: 4467-4476.
47. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, et al. (2006) 3′ UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nat Methods 3: 199-204.
48. de Jong JF, Deelstra HJ, Wosten HA, Lugones LG, (2006) RNA-mediated gene silencing in monokaryons and dikaryons of Schizophyllum commune. Appl Environ Microbiol 72: 1267-1269.
49. Fitzgerald A, Van Kan JA, Plummer KM, (2004) Simultaneous silencing of multiple genes in the apple scab fungus, Venturia inaequalis, by expression of RNA with chimeric inverted repeats. Fungal Genet Biol 41: 963-971.
50. Whisson SC, Avrova AO, West PN, Jones JT, (2005) A method for double-stranded RNA-mediated transient gene silencing in Phytophthora infestans. Mol Plant Pathol 6: 153-163.
51. Costa AM, Mills PR, Bailey AM, Foster GD, Challen MP, (2008) Oligonucleotide sequences forming short self-complimentary hairpins can expedite the down-regulation of Coprinopsis cinerea genes. J Microbiol Methods 75: 205-208.
52. Osherov N, May G, (2000) Conidial germination in Aspergillus nidulans requires RAS signaling and protein synthesis. Genetics 155: 647-656.
53. Kumar P, Pandit SS, Baldwin IT, (2012) Tobacco rattle virus vector: A Rapid and transient means of silencing Manduca sexta genes by plant mediated RNA interference. Plos One 7 (2): e31347 doi:10.1371/journal.pone.0031347.
54. Barratt RW, Johnson GB, Ogata WN, (1965) Wild-type and mutant stocks of Aspergillus nidulans. Genetics 52: 233-246.
55. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: A laboratory manual. Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory.