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Volumn 17, Issue 3, 2016, Pages

De novo transcriptome assembly in Shiraia bambusicola to investigate putative genes involved in the biosynthesis of hypocrellin A

Author keywords

Differentially expressed genes; RNA Seq; Shiraia bambusicola; Ultraviolet mutagenesis

Indexed keywords

HEME; HYPOCRELLIN A; OXIDOREDUCTASE; REACTIVE OXYGEN METABOLITE; TRANSCRIPTOME; PERYLENE; QUINONE DERIVATIVE;

EID: 84959332833     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms17030311     Document Type: Article
Times cited : (39)

References (42)
  • 1
    • 1842856199 scopus 로고    scopus 로고
    • Efficacy of hypocrellin pharmacokinetics in phototherapy
    • [CrossRef] [PubMed]
    • Ali, S.M.; Olivo, M. Efficacy of hypocrellin pharmacokinetics in phototherapy. Int. J. Oncol. 2002, 21, 1229-1237. [CrossRef] [PubMed]
    • (2002) Int. J. Oncol , vol.21 , pp. 1229-1237
    • Ali, S.M.1    Olivo, M.2
  • 2
    • 33845542867 scopus 로고    scopus 로고
    • Molecular diversity of bamboo-associated fungi isolated from Japan
    • [CrossRef] [PubMed]
    • Morakotkarn, D.; Kawasaki, H.; Seki, T. Molecular diversity of bamboo-associated fungi isolated from Japan. FEMS Microbiol. Lett. 2007, 266, 10-19. [CrossRef] [PubMed]
    • (2007) FEMS Microbiol. Lett , vol.266 , pp. 10-19
    • Morakotkarn, D.1    Kawasaki, H.2    Seki, T.3
  • 3
    • 0025492434 scopus 로고
    • Hypocrellins and their use in photosensitization
    • [CrossRef] [PubMed]
    • Zhenjun, D.; Lown, J.W. Hypocrellins and their use in photosensitization. Photochem. Photobiol. 1990, 52, 609-616. [CrossRef] [PubMed]
    • (1990) Photochem. Photobiol , vol.52 , pp. 609-616
    • Zhenjun, D.1    Lown, J.W.2
  • 5
    • 0028504737 scopus 로고
    • Hypocrellin, from Hypocrella bambuase, is phototoxic to human immunodeficiency virus
    • [CrossRef] [PubMed]
    • Hudson, J.; Zhou, J.; Chen, J.; Harris, L.; Yip, L.; Towers, G. Hypocrellin, from Hypocrella bambuase, is phototoxic to human immunodeficiency virus. Photochem. Photobiol. 1994, 60, 253-255. [CrossRef] [PubMed]
    • (1994) Photochem. Photobiol , vol.60 , pp. 253-255
    • Hudson, J.1    Zhou, J.2    Chen, J.3    Harris, L.4    Yip, L.5    Towers, G.6
  • 6
    • 0024116243 scopus 로고
    • Effect of hypocrellin A sensitization on the lateral mobility of cell membrane proteins
    • [CrossRef]
    • Longsheng, C.; Jiazhen, W.; Shimi, F. Effect of hypocrellin A sensitization on the lateral mobility of cell membrane proteins. J. Photochem. Photobiol. B 1988, 2, 395-398. [CrossRef]
    • (1988) J. Photochem. Photobiol. B , vol.2 , pp. 395-398
    • Longsheng, C.1    Jiazhen, W.2    Shimi, F.3
  • 7
    • 0036461958 scopus 로고    scopus 로고
    • The role of apoptosis in response to photodynamic therapy: What, where, why, and how
    • [PubMed]
    • Oleinick, N.L.; Morris, R.L.; Belichenko, I. The role of apoptosis in response to photodynamic therapy: What, where, why, and how. Photochem. Photobiol. Sci. 2002, 1, 1-21. [PubMed]
    • (2002) Photochem. Photobiol. Sci , vol.1 , pp. 1-21
    • Oleinick, N.L.1    Morris, R.L.2    Belichenko, I.3
  • 8
    • 67349201695 scopus 로고    scopus 로고
    • Photodynamic therapy (PDT): A short review on cellular mechanisms and cancer research applications for PDT
    • [CrossRef] [PubMed]
    • Robertson, C.; Evans, D.H.; Abrahamse, H. Photodynamic therapy (PDT): A short review on cellular mechanisms and cancer research applications for PDT. J. Photochem. Photobiol. B 2009, 96, 1-8. [CrossRef] [PubMed]
    • (2009) J. Photochem. Photobiol. B , vol.96 , pp. 1-8
    • Robertson, C.1    Evans, D.H.2    Abrahamse, H.3
  • 9
    • 84907159559 scopus 로고    scopus 로고
    • Preparation and evaluation of hypocrellin A loaded poly (Lactic-co-glycolic acid) nanoparticles for photodynamic therapy
    • [CrossRef]
    • Qi, S.S.; Lin, X.; Zhang, M.M.; Yan, S.Z.; Yu, S.Q.; Chen, S.L. Preparation and evaluation of hypocrellin A loaded poly (lactic-co-glycolic acid) nanoparticles for photodynamic therapy. RSC Adv. 2014, 4, 40085-40094. [CrossRef]
    • (2014) RSC Adv , vol.4 , pp. 40085-40094
    • Qi, S.S.1    Lin, X.2    Zhang, M.M.3    Yan, S.Z.4    Yu, S.Q.5    Chen, S.L.6
  • 10
    • 0027967263 scopus 로고
    • Phototherapeutic potential of alternative photosensitizers to porphyrins
    • [CrossRef]
    • Diwu, Z.; Lown, J.W. Phototherapeutic potential of alternative photosensitizers to porphyrins. Pharmacol. Ther. 1994, 63, 1-35. [CrossRef]
    • (1994) Pharmacol. Ther , vol.63 , pp. 1-35
    • Diwu, Z.1    Lown, J.W.2
  • 11
    • 0033738888 scopus 로고    scopus 로고
    • The photoactivated Cercospora toxin cercosporin: Contributions to plant disease and fundamental biology
    • [CrossRef] [PubMed]
    • Daub, M.E.; Ehrenshaft, M. The photoactivated Cercospora toxin cercosporin: Contributions to plant disease and fundamental biology. Annu. Rev. Phytopathol. 2000, 38, 461-490. [CrossRef] [PubMed]
    • (2000) Annu. Rev. Phytopathol , vol.38 , pp. 461-490
    • Daub, M.E.1    Ehrenshaft, M.2
  • 12
    • 0016617919 scopus 로고
    • Biosynthesis of cercosporin
    • [CrossRef]
    • Okubo, A.; Yamazaki, S.; Fuwa, K. Biosynthesis of cercosporin. Agric. Biol. Chem. 1975, 39, 1173-1175. [CrossRef]
    • (1975) Agric. Biol. Chem , vol.39 , pp. 1173-1175
    • Okubo, A.1    Yamazaki, S.2    Fuwa, K.3
  • 13
    • 17644387189 scopus 로고    scopus 로고
    • The ctb1 gene encoding a fungal polyketide synthase is required for cercosporin biosynthesis and fungal virulence of Cercospora nicotianae
    • [CrossRef] [PubMed]
    • Choquer, M.; Dekkers, K.L.; Chen, H.Q.; Cao, L.; Ueng, P.P.; Daub, M.E.; Chung, K.R. The ctb1 gene encoding a fungal polyketide synthase is required for cercosporin biosynthesis and fungal virulence of Cercospora nicotianae. Mol. Plant Microbe Interact. 2005, 18, 468-476. [CrossRef] [PubMed]
    • (2005) Mol. Plant Microbe Interact , vol.18 , pp. 468-476
    • Choquer, M.1    Dekkers, K.L.2    Chen, H.Q.3    Cao, L.4    Ueng, P.P.5    Daub, M.E.6    Chung, K.R.7
  • 14
    • 33846422996 scopus 로고    scopus 로고
    • The Cercospora nicotianae gene encoding dual O-methyltransferase and FAD-dependent monooxygenase domains mediates cercosporin toxin biosynthesis
    • [CrossRef] [PubMed]
    • Dekkers, K.L.; You, B.J.; Gowda, V.S.; Liao, H.L.; Lee, M.H.; Bau, H.J.; Ueng, P.P.; Chung, K.R. The Cercospora nicotianae gene encoding dual O-methyltransferase and FAD-dependent monooxygenase domains mediates cercosporin toxin biosynthesis. Fungal Genet. Biol. 2007, 44, 444-454. [CrossRef] [PubMed]
    • (2007) Fungal Genet. Biol , vol.44 , pp. 444-454
    • Dekkers, K.L.1    You, B.J.2    Gowda, V.S.3    Liao, H.L.4    Lee, M.H.5    Bau, H.J.6    Ueng, P.P.7    Chung, K.R.8
  • 15
    • 33846463440 scopus 로고    scopus 로고
    • Deletion of a MFS transporter-like gene in Cercospora nicotianae reduces cercosporin toxin accumulation and fungal virulence
    • [CrossRef] [PubMed]
    • Choquer, M.; Lee, M.H.; Bau, H.J.; Chung, K.R. Deletion of a MFS transporter-like gene in Cercospora nicotianae reduces cercosporin toxin accumulation and fungal virulence. FEBS Lett. 2007, 581, 489-494. [CrossRef] [PubMed]
    • (2007) FEBS Lett , vol.581 , pp. 489-494
    • Choquer, M.1    Lee, M.H.2    Bau, H.J.3    Chung, K.R.4
  • 16
    • 34247540410 scopus 로고    scopus 로고
    • Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae
    • [CrossRef] [PubMed]
    • Chen, H.; Lee, M.H.; Daub, M.E.; Chung, K.R. Molecular analysis of the cercosporin biosynthetic gene cluster in Cercospora nicotianae. Mol. Microbiol. 2007, 64, 755-770. [CrossRef] [PubMed]
    • (2007) Mol. Microbiol , vol.64 , pp. 755-770
    • Chen, H.1    Lee, M.H.2    Daub, M.E.3    Chung, K.R.4
  • 17
    • 34547901845 scopus 로고    scopus 로고
    • Functional characterization of three genes encoding putative oxidoreductases required for cercosporin toxin biosynthesis in the fungus Cercospora nicotianae
    • [CrossRef] [PubMed]
    • Chen, H.Q.; Lee, M.H.; Chung, K.R. Functional characterization of three genes encoding putative oxidoreductases required for cercosporin toxin biosynthesis in the fungus Cercospora nicotianae. Microbiology 2007, 153, 2781-2790. [CrossRef] [PubMed]
    • (2007) Microbiology , vol.153 , pp. 2781-2790
    • Chen, H.Q.1    Lee, M.H.2    Chung, K.R.3
  • 18
    • 0033215141 scopus 로고    scopus 로고
    • Cfp, the putative cercosporin transporter of Cercospora kikuchii, is required for wild type cercosporin production, resistance, and virulence on soybean
    • [CrossRef] [PubMed]
    • Callahan, T.M.; Rose, M.S.; Meade, M.J.; Ehrenshaft, M.; Upchurch, R.G. Cfp, the putative cercosporin transporter of Cercospora kikuchii, is required for wild type cercosporin production, resistance, and virulence on soybean. Mol. Plant Microbe Interact. 1999, 12, 901-910. [CrossRef] [PubMed]
    • (1999) Mol. Plant Microbe Interact , vol.12 , pp. 901-910
    • Callahan, T.M.1    Rose, M.S.2    Meade, M.J.3    Ehrenshaft, M.4    Upchurch, R.G.5
  • 19
    • 84977867669 scopus 로고    scopus 로고
    • Preliminary study on one polyketide synthase from Shiraia sp. SUPER-H168
    • Chang, K.M.; Deng, H.X.; Guan, Z.B.; Liao, X.R.; Cai, Y.J. Preliminary study on one polyketide synthase from Shiraia sp. SUPER-H168. Biotechnology 2014, 1-4.
    • (2014) Biotechnology , pp. 1-4
    • Chang, K.M.1    Deng, H.X.2    Guan, Z.B.3    Liao, X.R.4    Cai, Y.J.5
  • 20
    • 84977839958 scopus 로고    scopus 로고
    • The prokaryotic expression, purification and bioinformatics of type III polyketide synthase from Shiraia sp. Slf14, which is an endophytic fungus of Huperzia serrata
    • Peng, S.L.; Yang, H.L.; Li, E.H.; Wang, X.L.; Zhu, D. The prokaryotic expression, purification and bioinformatics of type III polyketide synthase from Shiraia sp. Slf14, which is an endophytic fungus of Huperzia serrata. J. Jiangxi Norm. Univ. 2015, 39, 430-434.
    • (2015) J. Jiangxi Norm. Univ , vol.39 , pp. 430-434
    • Peng, S.L.1    Yang, H.L.2    Li, E.H.3    Wang, X.L.4    Zhu, D.5
  • 21
    • 57749195712 scopus 로고    scopus 로고
    • RNA-seq: A revolutionary tool for transcriptomics. Nat
    • [CrossRef] [PubMed]
    • Wang, Z.; Gerstein, M.; Snyder, M. RNA-seq: A revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10, 57-63. [CrossRef] [PubMed]
    • (2009) Rev. Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 22
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • [CrossRef] [PubMed]
    • Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 2000, 28, 27-30. [CrossRef] [PubMed]
    • (2000) Nucleic Acids Res , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 24
    • 78449260597 scopus 로고    scopus 로고
    • Photoactivated perylenequinone toxins in plant pathogenesis
    • Daub, M.E.; Chung, K.R. Photoactivated perylenequinone toxins in plant pathogenesis. Plant Relatsh. 2009, 5, 201-219.
    • (2009) Plant Relatsh , vol.5 , pp. 201-219
    • Daub, M.E.1    Chung, K.R.2
  • 25
    • 0000439483 scopus 로고
    • Photodynamic action
    • [CrossRef]
    • Valenzeno, D.P.; Pooler, J.P. Photodynamic action. BioScience 1987, 37, 270-276. [CrossRef]
    • (1987) Bioscience , vol.37 , pp. 270-276
    • Valenzeno, D.P.1    Pooler, J.P.2
  • 26
    • 84944510899 scopus 로고    scopus 로고
    • Membrane transporters in self resistance of Cercospora nicotianae to the photoactivated toxin cercosporin
    • [CrossRef] [PubMed]
    • Beseli, A.; Amnuaykanjanasin, A.; Herrero, S.; Thomas, E.; Daub, M.E. Membrane transporters in self resistance of Cercospora nicotianae to the photoactivated toxin cercosporin. Curr. Genet. 2015, 61, 601-620. [CrossRef] [PubMed]
    • (2015) Curr. Genet , vol.61 , pp. 601-620
    • Beseli, A.1    Amnuaykanjanasin, A.2    Herrero, S.3    Thomas, E.4    Daub, M.E.5
  • 27
    • 0000861423 scopus 로고
    • Physical quenchers of singlet molecular oxygen
    • Belluš, D. Physical quenchers of singlet molecular oxygen. Adv. Photochem. 1978, 11, 105-205.
    • (1978) Adv. Photochem , vol.11 , pp. 105-205
    • Belluš, D.1
  • 28
    • 0000034450 scopus 로고
    • Carotenoid protection against oxidation
    • [CrossRef]
    • Krinsky, N.I. Carotenoid protection against oxidation. Pure Appl. Chem. 1979, 51, 649-660. [CrossRef]
    • (1979) Pure Appl. Chem , vol.51 , pp. 649-660
    • Krinsky, N.I.1
  • 29
    • 0027218691 scopus 로고
    • Actions of carotenoids in biological systems
    • [CrossRef][PubMed]
    • Krinsky, N.I. Actions of carotenoids in biological systems. Annu. Rev. Nutr. 1993, 13, 561-587. [CrossRef][PubMed]
    • (1993) Annu. Rev. Nutr , vol.13 , pp. 561-587
    • Krinsky, N.I.1
  • 30
    • 0000412002 scopus 로고
    • The photoprotective role of carotenoids in higher plants
    • [CrossRef]
    • Young, A.J. The photoprotective role of carotenoids in higher plants. Physiol. Plant. 1991, 83, 702-708. [CrossRef]
    • (1991) Physiol. Plant , vol.83 , pp. 702-708
    • Young, A.J.1
  • 31
    • 0033529936 scopus 로고    scopus 로고
    • A highly conserved sequence is a novel gene involved in de novo vitamin b6 biosynthesis
    • [CrossRef] [PubMed]
    • Ehrenshaft, M.; Bilski, P.; Li, M.Y.; Chignell, C.F.; Daub, M.E. A highly conserved sequence is a novel gene involved in de novo vitamin b6 biosynthesis. Proc. Natl. Acad. Sci. USA 1999, 96, 9374-9378. [CrossRef] [PubMed]
    • (1999) Proc. Natl. Acad. Sci. USA , vol.96 , pp. 9374-9378
    • Ehrenshaft, M.1    Bilski, P.2    Li, M.Y.3    Chignell, C.F.4    Daub, M.E.5
  • 32
    • 0035025630 scopus 로고    scopus 로고
    • Isolation of pdx2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria
    • [CrossRef] [PubMed]
    • Ehrenshaft, M.; Daub, M.E. Isolation of pdx2, a second novel gene in the pyridoxine biosynthesis pathway of eukaryotes, archaebacteria, and a subset of eubacteria. J. Bacteriol. 2001, 183, 3383-3390. [CrossRef] [PubMed]
    • (2001) J. Bacteriol. , vol.183 , pp. 3383-3390
    • Ehrenshaft, M.1    Daub, M.E.2
  • 33
    • 0034132391 scopus 로고    scopus 로고
    • Vitamin b6 (Pyridoxine) and its derivatives are efficient singlet oxygen quenchers and potential fungal antioxidants
    • [CrossRef]
    • Bilski, P.; Li, M.; Ehrenshaft, M.; Daub, M.; Chignell, C. Vitamin b6 (pyridoxine) and its derivatives are efficient singlet oxygen quenchers and potential fungal antioxidants. Photochem. Photobiol. 2000, 71, 129-134. [CrossRef]
    • (2000) Photochem. Photobiol , vol.71 , pp. 129-134
    • Bilski, P.1    Li, M.2    Ehrenshaft, M.3    Daub, M.4    Chignell, C.5
  • 34
    • 28944438321 scopus 로고    scopus 로고
    • Regulation of biosynthetic genes and antioxidant properties of vitamin B6 vitamers during plant defense responses
    • [CrossRef]
    • Denslow, S.A.; Walls, A.A.; Daub, M.E. Regulation of biosynthetic genes and antioxidant properties of vitamin B6 vitamers during plant defense responses. Physiol. Mol. Plant Pathol. 2005, 66, 244-255. [CrossRef]
    • (2005) Physiol. Mol. Plant Pathol. , vol.66 , pp. 244-255
    • Denslow, S.A.1    Walls, A.A.2    Daub, M.E.3
  • 35
    • 84989719170 scopus 로고
    • Singlet oxygen yields, optical properties, and phototoxicity of reduced derivatives of the photosensitizer cercosporin
    • [CrossRef]
    • Leisman, G.B.; Daub, M.E. Singlet oxygen yields, optical properties, and phototoxicity of reduced derivatives of the photosensitizer cercosporin. Photochem. Photobiol. 1992, 55, 373-379. [CrossRef]
    • (1992) Photochem. Photobiol , vol.55 , pp. 373-379
    • Leisman, G.B.1    Daub, M.E.2
  • 36
    • 0026593510 scopus 로고
    • Cell surface redox potential as a mechanism of defense against photosensitizers in fungi
    • [PubMed]
    • Sollod, C.C.; Jenns, A.E.; Daub, M.E. Cell surface redox potential as a mechanism of defense against photosensitizers in fungi. Appl. Environ. Microbiol. 1992, 58, 444-449 [PubMed]
    • (1992) Appl. Environ. Microbiol , vol.58 , pp. 444-449
    • Sollod, C.C.1    Jenns, A.E.2    Daub, M.E.3
  • 37
    • 80052962498 scopus 로고    scopus 로고
    • Induction of hypocrellin production by Triton X-100 under submerged fermentation with Shiraia sp. SUPER-H168
    • [CrossRef] [PubMed]
    • Cai, Y.; Liao, X.; Liang, X.; Ding, Y.; Sun, J.; Zhang, D. Induction of hypocrellin production by Triton X-100 under submerged fermentation with Shiraia sp. SUPER-H168. N. Biotechnol. 2011, 28, 588-592. [CrossRef] [PubMed]
    • (2011) N. Biotechnol , vol.28 , pp. 588-592
    • Cai, Y.1    Liao, X.2    Liang, X.3    Ding, Y.4    Sun, J.5    Zhang, D.6
  • 39
    • 24644503098 scopus 로고    scopus 로고
    • Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research
    • [CrossRef] [PubMed]
    • Conesa, A.; Götz, S.; García-Gómez, J.M.; Terol, J.; Talón, M.; Robles, M. Blast2GO: A universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21, 3674-3676. [CrossRef] [PubMed]
    • (2005) Bioinformatics , vol.21 , pp. 3674-3676
    • Conesa, A.1    Götz, S.2    García-Gómez, J.M.3    Terol, J.4    Talón, M.5    Robles, M.6
  • 40
    • 46249106990 scopus 로고    scopus 로고
    • Mapping and quantifying mammalian transcriptomes by RNA-seq
    • [CrossRef] [PubMed]
    • Mortazavi, A.; Williams, B.A.; McCue, K.; Schaeffer, L.; Wold, B. Mapping and quantifying mammalian transcriptomes by RNA-seq. Nat. Methods 2008, 5, 621-628. [CrossRef] [PubMed]
    • (2008) Nat. Methods , vol.5 , pp. 621-628
    • Mortazavi, A.1    Williams, B.A.2    McCue, K.3    Schaeffer, L.4    Wold, B.5
  • 41
    • 45549088326 scopus 로고    scopus 로고
    • The transcriptional landscape of the yeast genome defined by RNA sequencing
    • [CrossRef] [PubMed]
    • Nagalakshmi, U.; Wang, Z.; Waern, K.; Shou, C.; Raha, D.; Gerstein, M.; Snyder, M. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 2008, 320, 1344-1349. [CrossRef] [PubMed]
    • (2008) Science , vol.320 , pp. 1344-1349
    • Nagalakshmi, U.1    Wang, Z.2    Waern, K.3    Shou, C.4    Raha, D.5    Gerstein, M.6    Snyder, M.7
  • 42
    • 0035710746 scopus 로고    scopus 로고
    • Analysis of relative gene expression data using Real-time quantitative PCR and the 2´ΔΔCt method
    • [CrossRef] [PubMed]
    • Livak, K.J.; Schmittgen, T.D. Analysis of relative gene expression data using Real-time quantitative PCR and the 2´ΔΔCt method. Methods 2001, 25, 402-408. [CrossRef] [PubMed]
    • (2001) Methods , vol.25 , pp. 402-408
    • Livak, K.J.1    Schmittgen, T.D.2


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