Applied Microbiology and Biotechnology

, Volume 97, Issue 11, pp 4977–4989

Transcriptome analysis of candidate genes and signaling pathways associated with light-induced brown film formation in Lentinula edodes

  • Li-hua Tang
  • Hua-hua Jian
  • Chun-yan Song
  • Da-peng Bao
  • Xiao-dong Shang
  • Da-qiang Wu
  • Qi Tan
  • Xue-hong Zhang
Genomics, transcriptomics, proteomics

Abstract

High-throughput Illumina RNA-seq was used for deep sequencing analysis of the transcriptome of poly(A)+ RNA from mycelium grown under three different conditions: 30 days darkness (sample 118), 80 days darkness (313W), and 30 days darkness followed by 50 days in the light (313C), in order to gain insight into the molecular mechanisms underlying the process of light-induced brown film (BF) formation in the edible mushroom, Lentinula edodes. Of the three growth conditions, BF formation occurred in 313C samples only. Approximately 159.23 million reads were obtained, trimmed, and de novo assembled into 31,511 contigs with an average length of 1,746 bp and an N50 of 2,480 bp. Based on sequence orientations determined by a BLASTX search against the NR, Swiss-Prot, COG, and KEGG databases, 24,246 (76.9 %) contigs were assigned putative descriptions. Comparison of 313C/118 and 313C/313W expression profiles revealed 3,958 and 5,651 significantly differentially expressed contigs (DECs), respectively. Annotation using the COG database revealed that candidate genes for light-induced BF formation encoded proteins linked to light reception (e.g., WC-1, WC-2, phytochrome), light signal transduction pathways (e.g., two-component phosphorelay system, mitogen-activated protein kinase pathway), and pigment formation (e.g., polyketide synthase, O-methyltransferase, laccase, P450 monooxygenase, oxidoreductase). Several DECs were validated using quantitative real-time polymerase chain reaction. Our report is the first to identify genes associated with light-induced BF formation in L. edodes and represents a valuable resource for future genomic studies on this commercially important mushroom.

Keywords

Lentinula edodes Light-induced brown film formation Transcriptome Differential expression 

Supplementary material

253_2013_4832_MOESM1_ESM.pdf (281 kb)
ESM 1(PDF 281 kb)

References

  1. Aleksandrova EA, Zav’yalova LA, Tereshina VM, Garibova LV, Feofilova EP (1998) Obtaining of fruiting bodies and submerged mycelium of Lentinus edodes (Berk.) Sing [Lentinula edodes (Berk.) Pegler]. Microbiology 67:535–539Google Scholar
  2. Atoui A, Bao DP, Kaur N, Grayburn WS, Calvo AM (2008) Aspergillus nidulans natural product biosynthesis is regulated by mpkB, a putative pheromone response mitogen-activated protein kinase. Appl Environ Microbiol 74:3596–3600CrossRefGoogle Scholar
  3. Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995Google Scholar
  4. Ballario P, Vittorioso P, Magrelli A, Talora C, Cabibbo A, Macinol G (1996) White collar-1, a central regulator of blue light responses in Neurospora, is a zinc finger protein. EMBO J 15:1650–1657Google Scholar
  5. Bayram Ö, Braus GH (2012) Coordination of secondary metabolism and development in fungi: the velvet family of regulatory proteins. FEMS Microbiol Rev 36:1–24CrossRefGoogle Scholar
  6. Bayram Ö, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, Braus-Stromeyer S, Kwon NJ, Keller NP, Yu JH, Braus GH (2008) VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science 320:1504–1506CrossRefGoogle Scholar
  7. Bayram Ö, Bayram ÖS, Ahmed YL, Maruyama JI, Valerius O, Rizzoli SO, Ficner R, Irniger S, Braus GH (2012) The Aspergillus nidulans MAPK module AnSte11-Ste50-Ste7-Fus3 controls development and secondary metabolism. PLoS Genet 8:e1002816CrossRefGoogle Scholar
  8. Bhatnagar D, Ehrlich KC, Cleveland TE (2003) Molecular genetic analysis and regulation of aflatoxin biosynthesis. Appl Microbiol Biotechnol 61:83–93Google Scholar
  9. Blumenstein A, Vienken K, Tasler R, Purschwitz J, Veith D, Nicole FD, Fischer R (2005) The Aspergillus nidulans phytochrome fphA represses sexual development in red light. Curr Biol 15:1833–1838CrossRefGoogle Scholar
  10. Chen RE, Thorner J (2007) Function and regulation in MAPK signaling pathways: lessons learned from the yeast Saccharomyces cerevisiae. Biochim Biophys Acta 1773:1311–1340CrossRefGoogle Scholar
  11. Chen SC, Ge W, Buswell JA (2004) Molecular cloning of a new laccase from the edible straw mushroom Volvariella volvacea: possible involvement in fruit body development. FEMS Microbiol Lett 230:171–176CrossRefGoogle Scholar
  12. Chum WWY, Ng KTP, Shih RSM, Au CH, Kwan HS (2008) Gene expression studies of the dikaryotic mycelium and primordium of Lentinula edodes by serial analysis of gene expression. Mycol Res 112:950–964CrossRefGoogle Scholar
  13. Chum WWY, Kwan HS, Au CH, Kwok ISW, Fung YW (2011) Cataloging and profiling genes expressed in Lentinula edodes fruiting body by massive cDNA pyrosequencing and LongSAGE. Fungal Genet Biol 48:359–369CrossRefGoogle Scholar
  14. de Paula RM, Lamb TM, Bennett L, Bell-Pedersen D (2008) A connection between MAPK pathways and circadian clocks. Cell Cycle 7:2630–2634CrossRefGoogle Scholar
  15. Drepper T, Krauss U, Meyer zu Berstenhorst S, Pietruszka J, Jaeger KE (2011) Lights on and action! Controlling microbial gene expression by light. Appl Microbiol Biotechnol 90:23–40CrossRefGoogle Scholar
  16. Estrada AF, Avalos J (2008) The White Collar protein WcoA of Fusarium fujikuroi is not essential for photocarotenogenesis, but is involved in the regulation of secondary metabolism and conidiation. Fungal Genet Biol 45:705–718CrossRefGoogle Scholar
  17. Frandsen RJN, Nielsen NJ, Maolanon N, Sørensen JC, Olsson S, Nielsen J, Giese H (2006) The biosynthetic pathway for aurofusarin in Fusarium graminearum reveals a close link between the naphthoquinones and naphthopyrones. Mol Microbiol 61:1069–1080CrossRefGoogle Scholar
  18. Froehlich AC, Noh B, Vierstra RD, Loros J, Dunlap JC (2005) Genetic and molecular analysis of phytochromes from the filamentous fungus Neurospora crassa. Eukaryot Cell 4:2140–2152CrossRefGoogle Scholar
  19. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng QD, Chen ZH, Mauceli E, Hacohen N, Gnirke A, Rhind N, Palma FD, Birren BW, Nusbaum C, Lindblad-Toh K, Friedman N, Regev A (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652CrossRefGoogle Scholar
  20. Hoffmeister D, Keller NP (2007) Natural products of filamentous fungi: enzymes, genes, and their regulation. Nat Prod Rep 24:393–416CrossRefGoogle Scholar
  21. Huang JW, Chen WC, Huang TK, Fu PS, Lai PL, Tsai CF, Hung CC (2011) Using a spectrophotometric study of human gingival color distribution to develop a shade guide. J Dent 39:e11–e16CrossRefGoogle Scholar
  22. Idnurm A, Heitman J (2005) Light controls growth and development via a conserved pathway in the fungal kingdom. PLos Biol 3:e95CrossRefGoogle Scholar
  23. Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res 28:27–30CrossRefGoogle Scholar
  24. Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M (2012) KEGG for integration and interpretation of large-scale molecular datasets. Nucleic Acids Res 40:109–114CrossRefGoogle Scholar
  25. Keller NP, Hohn TM (1997) Metabolic pathway gene clusters in filamentous fungi. Fungal Genet Biol 21:17–29CrossRefGoogle Scholar
  26. Kumar S, Tamura K, Nei M (2004) MEGA3: integrated software for molecular evolutionary genetics analysis and sequence alignment. Brief Bioinform 5:150–163CrossRefGoogle Scholar
  27. Kuratani M, Tanaka K, Terashima K, Muraguchi H, Nakazawa T, Nakahori K, Kamada T (2010) The dst2 gene essential for photomorphogenesis of Coprinopsis cinerea encodes a protein with a putative FAD-binding-4 domain. Fungal Genet Biol 47:152–158CrossRefGoogle Scholar
  28. Leatham G, Stahmann MA (1981) Studies on the laccase of Lentinus edodes: specificity, localization and association with the development of fruiting bodies. J Gen Microbiol 125:147–157Google Scholar
  29. Lee SS, Hong SW, Kim SH, Kim BC (2001) Several genes expressed during morphogenesis of Lentinus edodes (ImHyup-1). Mycobiology 29:135–141Google Scholar
  30. Li HY, Dong YY, Yang J, Liu XM, Wang YF, Yao N, Guan LL, Wang N, Wu JY, Li XK (2012) De novo transcriptome of safflower and the identification of putative genes for oleosin and the biosynthesis of flavonoids. PLoS One 7:e30987CrossRefGoogle Scholar
  31. Linden H, Macino G (1997) White collar 2, a partner in blue-light signal transduction, controlling expression of light-regulated genes in Neurospora crassa. EMBO J 16:98–109CrossRefGoogle Scholar
  32. Linnemannstöns P, Schulte J, del Mar PM, Proctor RH, Avalos J, Tudzynski B (2002) The polyketide synthase gene pks4 from Gibberella fujikuroi encodes a key enzyme in the biosynthesis of the red pigment bikaverin. Fungal Genet Biol 37:134–148CrossRefGoogle Scholar
  33. Liu WW, Soulié MC, Perrino C, Fillinger S (2011) The osmosensing signal transduction pathway from Botrytis cinerea regulates cell wall integrity and MAP kinase pathways control melanin biosynthesis with influence of light. Fungal Genet Biol 48:377–387CrossRefGoogle Scholar
  34. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25:402–408CrossRefGoogle Scholar
  35. Miyazaki Y, Nakamura M, Babasaki K (2005) Molecular cloning of developmentally specific genes by representational difference analysis during the fruiting body formation in the basidiomycete Lentinula edodes. Fungal Genet Biol 42:493–505CrossRefGoogle Scholar
  36. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B (2008) Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5:621–628CrossRefGoogle Scholar
  37. Nagalakshmi U, Wang Z, Waern K, Shou C, Raha D, Gerstein M, Snyder M (2008) The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320:1344–1349CrossRefGoogle Scholar
  38. Ohga S, Cho NS, Thurston CF, Wood DA (2000) Transcriptional regulation of laccase and cellulase in relation to fruit body formation in the mycelium of Lentinula edodes on a sawdust-based substrate. Mycoscience 41:149–153CrossRefGoogle Scholar
  39. Pertea G, Huang XQ, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652CrossRefGoogle Scholar
  40. Purschwitz J, Müller S, Kastner C, Schöser M, Haas H, Espeso EA, Atoui A, Calvo AM, Fischer R (2008) Functional and physical interaction of blue- and red-light sensors in Aspergillus nidulans. Curr Biol 18:255–259CrossRefGoogle Scholar
  41. Rodgers CJ, Blanford CF, Giddens SR, Skamnioti P, Armstrong FA, Gurr SJ (2010) Designer laccases: a vogue for high-potential fungal enzymes. Trends Biotechnol 28:63–72CrossRefGoogle Scholar
  42. Sakamoto Y, Nakade K, Sato T (2009) Characterization of the post-harvest changes in gene transcription in the gill of the Lentinula edodes fruiting body. Curr Genet 55:409–423CrossRefGoogle Scholar
  43. Sano H, Narikiyo T, Kaneko S, Yamazaki T, Shishido K (2007) Sequence analysis and expression of a blue-light photoreceptor gene, Le.phrA from the basidiomycetous mushroom Lentinula edodes. Biosci Biotech Biochem 71:2206–2213CrossRefGoogle Scholar
  44. Sano H, Kaneko S, Sakamoto Y, Sato T, Shishido K (2009) The basidiomycetous mushroom Lentinula edodes white collar-2 homolog PHRB, a partner of putative blue-light photoreceptor PHRA, binds to a specific site in the promoter region of the L. edodes tyrosinase gene. Fungal Genet Biol 46:333–341CrossRefGoogle Scholar
  45. Suizu T, Zhou GL, Oowatari Y, Kawamukai M (2008) Analysis of expressed sequence tags (ESTs) from Lentinula edodes. Appl Microbiol Biotechnol 79:461–470CrossRefGoogle Scholar
  46. Szeto CYY, Wong QWL, Leung GS, Kwan HS (2008) Isolation and transcript analysis of two-component histidine kinase gene Le.nik1 in Shiitake mushroom, Lentinula edodes. Mycol Res 112:108–116CrossRefGoogle Scholar
  47. Takano Y, Kikuchi T, Kubo Y, Hamer JE, Mise K, Furusawa I (2000) The Colletotrichum lagenarium MAP kinase gene CMK1 regulates diverse aspects of fungal pathogenesis. Mol Plant Microbe Interact 13:374–383CrossRefGoogle Scholar
  48. Terashima K, Yuki K, Muraguchi H, Akiyama M, Kamada T (2005) The dst1 gene involved in mushroom photomorphogenesis of Coprinus cinereus encodes a putative photoreceptor for blue light. Genetics 171:101–108CrossRefGoogle Scholar
  49. Tisch D, Schmoll M (2010) Light regulation of metabolic pathways in fungi. Appl Microbiol Biotechnol 85:1259–1277CrossRefGoogle Scholar
  50. Tsivileva OM, Pankratov AN, Nikitina VE, Garibova LV (2005) Effect of media components on the mycelial film formation in submerged culture of Lentinus edodes (Shiitake). Food Technol Biotech 43:227–234Google Scholar
  51. Wang B, Guo GW, Wang C, Lin Y, Wang XN, Zhao MM, Guo Y, He MH, Zhang Y, Pan L (2010a) Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res 38:5075–5087CrossRefGoogle Scholar
  52. Wang XW, Luan JB, Li JM, Bao YY, Zhang CX, Liu SS (2010b) De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics 11:400CrossRefGoogle Scholar
  53. West AH, Stock AM (2001) Histidine kinases and response regulator proteins in two-component signaling systems. Trends Biochem Sci 26:369–376CrossRefGoogle Scholar
  54. Wong MML, Cannon CH, Wickneswari R (2011) Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing. BMC Genomics 12:342CrossRefGoogle Scholar
  55. Wu T, Qin ZW, Zhou XY, Feng Z, Du YL (2010) Transcriptome profile analysis of floral sex determination in cucumber. J Plant Physiol 167:905–913CrossRefGoogle Scholar
  56. Yu JJ, Fedorova ND, Montalbano BG, Bhatnagar D, Cleveland TE, Bennett JW, Nierman WC (2011) Tight control of mycotoxin biosynthesis gene expression in Aspergillus flavus by temperature as revealed by RNA-Seq. FEMS Microbiol Lett 322:145–149CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Li-hua Tang
    • 1
    • 2
  • Hua-hua Jian
    • 1
  • Chun-yan Song
    • 2
  • Da-peng Bao
    • 2
  • Xiao-dong Shang
    • 2
  • Da-qiang Wu
    • 1
  • Qi Tan
    • 2
  • Xue-hong Zhang
    • 1
  1. 1.State Key Laboratory of Microbial Metabolism, School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghaiPeople’s Republic of China
  2. 2.National Engineering Research Center of Edible Fungi, Key Laboratory of Edible Fungi Resources and Utilization (South), Ministry of Agriculture, Institute of Edible FungiShanghai Academy of Agricultural SciencesShanghaiPeople’s Republic of China

Personalised recommendations