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High throughput de novo RNA sequencing elucidates novel responses in Penicillium chrysogenum under microgravity

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Abstract

In this study, the transcriptional alterations in Penicillium chrysogenum under simulated microgravity conditions were analyzed for the first time using an RNA-Seq method. The increasing plethora of eukaryotic microbial flora inside the spaceship demands the basic understanding of fungal biology in the absence of gravity vector. Penicillium species are second most dominant fungal contaminant in International Space Station. Penicillium chrysogenum an industrially important organism also has the potential to emerge as an opportunistic pathogen for the astronauts during the long-term space missions. But till date, the cellular mechanisms underlying the survival and adaptation of Penicillium chrysogenum to microgravity conditions are not clearly elucidated. A reference genome for Penicillium chrysogenum is not yet available in the NCBI database. Hence, we performed comparative de novo transcriptome analysis of Penicillium chrysogenum grown under microgravity versus normal gravity. In addition, the changes due to microgravity are documented at the molecular level. Increased response to the environmental stimulus, changes in the cell wall component ABC transporter/MFS transporters are noteworthy. Interestingly, sustained increase in the expression of Acyl-coenzyme A: isopenicillin N acyltransferase (Acyltransferase) under microgravity revealed the significance of gravity in the penicillin production which could be exploited industrially.

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References

  1. Nickerson CA, Ott CM, Mister SJ, Morrow BJ, Burns-Keliher L, Pierson DL (2000) Microgravity as a novel environmental signal affecting Salmonella enterica serovar Typhimurium virulence. Infect Immun 68:3147–3152

    Article  CAS  Google Scholar 

  2. Rosado H, Doyle M, Hinds J, Taylor PW (2010) Low-shear modelled microgravity alters expression of virulence determinants of Staphylococcus aureus. Acta Astronaut 66:408–413

    Article  CAS  Google Scholar 

  3. Sathishkumar Y, Velmurugan N, Lee HM, Rajagopal K, Im CK, Lee YS (2014) Effect of low shear modeled microgravity on phenotypic and central chitin metabolism in the filamentous fungi Aspergillus niger and Penicillium chrysogenum. Antonie van Leeuwenhoek, 1–13

  4. Scalzi G, Selbmann L, Zucconi L, Rabbow E, Horneck G, Albertano P, Onofri S (2012) LIFE Experiment: isolation of cryptoendolithic organisms from Antarctic colonized sandstone exposed to space and simulated Mars conditions on the international space station. Orig Life Evol Biosph 42:253–262

    Article  Google Scholar 

  5. Stöffler D, Horneck G, Ott S, Hornemann U, Cockell CS, Moeller R, Meyer C, de Vera J-P, Fritz J, Artemieva NA (2007) Experimental evidence for the potential impact ejection of viable microorganisms from Mars and Mars-like planets. Icarus 186:585–588

    Article  Google Scholar 

  6. Onofri S, de la Torre R, de Vera J-P, Ott S, Zucconi L, Selbmann L, Scalzi G, Venkateswaran KJ, Rabbow E, Sánchez Iñigo FJ (2012) Survival of rock-colonizing organisms after 1.5 years in outer space. Astrobiology 12:508–516

    Article  Google Scholar 

  7. Onofri S, Barreca D, Selbmann L, Isola D, Rabbow E, Horneck G, De Vera J, Hatton J, Zucconi L (2008) Resistance of Antarctic black fungi and cryptoendolithic communities to simulated space and Martian conditions. Stud Mycol 61:99–109

    Article  CAS  Google Scholar 

  8. Novikova N (2004) Review of the knowledge of microbial contamination of the Russian manned spacecraft. Microb Ecol 47:127–132

    Article  CAS  Google Scholar 

  9. Tesei D, Marzban G, Zakharova K, Isola D, Selbmann L, Sterflinger K (2012) Alteration of protein patterns in black rock inhabiting fungi as a response to different temperatures. Fungal Biol 116:932–940

    Article  CAS  Google Scholar 

  10. Morabito C, Steimberg N, Mazzoleni G, Guarnieri S, Fanò-Illic G, Mariggiò MA (2015) RCCS bioreactor-based modelled microgravity induces significant changes on in vitro 3D neuroglial cell cultures. BioMed Res Int 2015

  11. Vunjak-novakovic G, Searby N, de Luis J, Freed LE (2002) Microgravity studies of cells and tissues. Ann N Y Acad Sci 974:504–517

    Article  Google Scholar 

  12. Fengler S, Spirer I, Neef M, Ecke M, Nieselt K, Hampp R (2015) A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8. BioMed Res Int 2015

  13. Chao T-C, Das DB (2015) Numerical simulation of coupled cell motion and nutrient transport in NASA’s rotating bioreactor. Chem Eng J 259:961–971

    Article  CAS  Google Scholar 

  14. Rösner H, Wassermann T, Möller W, Hanke W (2006) Effects of altered gravity on the actin and microtubule cytoskeleton of human SH-SY5Y neuroblastoma cells. Protoplasma 229:225–234

    Article  Google Scholar 

  15. Hoffman M, Bash E, Berger SA, Burke M, Yust I (1992) Fatal necrotizing esophagitis due to Penicillium chrysogenum in a patient with acquired immunodeficiency syndrome. Eur J Clin Microbiol Infect Dis 11:1158–1160

    Article  CAS  Google Scholar 

  16. Eschete ML, King JW, West BC, Oberle A (1981) Penicillium chrysogenum endophthalmitis. Mycopathologia 74:125–127

    Article  CAS  Google Scholar 

  17. D’Antonio D, Violante B, Farina C, Sacco R, Angelucci D, Masciulli M, Iacone A, Romano F (1997) Necrotizing pneumonia caused by Penicillium chrysogenum. J Clin Microbiol 35:3335–3337

    Google Scholar 

  18. López M, Neumann González M (1999) Case report: cutaneous penicilliosis due to Penicillium chrysogenum. Mycoses 42:347–349

    Article  Google Scholar 

  19. Inoue Y, Matsuwaki Y, Shin S-H, Ponikau JU, Kita H (2005) Nonpathogenic, environmental fungi induce activation and degranulation of human eosinophils. J Immunol 175:5439–5447

    Article  CAS  Google Scholar 

  20. Shen HD, Chou H, Tam M, Chang CY, Lai HY, Wang SR (2003) Molecular and immunological characterization of Pen ch 18, the vacuolar serine protease major allergen of Penicillium chrysogenum. Allergy 58:993–1002

    Article  CAS  Google Scholar 

  21. Shen HD, Liaw SF, Lin WL, Ro LH, Yang HL, Han SH (1995) Molecular cloning of cDNA coding for the 68 kDa allergen of Penicillium notatum using MoAbs. Clin Exp Allergy 25:350–356

    Article  CAS  Google Scholar 

  22. Kumar YS, Unnithan AR, Sen D, Kim CS, Lee YS (2015) Microgravity biosynthesized penicillin loaded electrospun polyurethane–dextran nanofibrous mats for biomedical applications. Colloids Surf A Physicochem Eng Asp 477:77–83

    Article  CAS  Google Scholar 

  23. Zakharova K, Marzban G, de Vera JP, Lorek A, Sterflinger K (2014) Protein patterns of black fungi under simulated Mars-like conditions. Sci Rep 4

  24. Morozova O, Marra MA (2008) Applications of next-generation sequencing technologies in functional genomics. Genomics 92:255–264

    Article  CAS  Google Scholar 

  25. Guo S, Zheng Y, Joung J-G, Liu S, Zhang Z, Crasta OR, Sobral BW, Xu Y, Huang S, Fei Z (2010) Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types. BMC Genom 11:384

    Article  CAS  Google Scholar 

  26. Feldmeyer B, Wheat CW, Krezdorn N, Rotter B, Pfenninger M (2011) Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance. BMC Genom 12:317

    Article  Google Scholar 

  27. Babraham FastQC. http://www.bioinformatiSample1.babraham.ac.uk/projects/fastqc/

  28. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, Amit I, Adiconis X, Fan L, Raychowdhury R, Zeng Q (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29:644–652

    Article  CAS  Google Scholar 

  29. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    Article  CAS  Google Scholar 

  30. Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M (2007) KAAS: an automatic genome annotation and pathway reconstruction server. Nucl Acids Res 35:W182–W185

    Article  Google Scholar 

  31. Li W, Jaroszewski L, Godzik A (2001) Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17:282–283

    Article  CAS  Google Scholar 

  32. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  Google Scholar 

  33. Anders S, Huber W (2010) Differential expression analysis for sequence count data. Genome Biol 11:R106

    Article  CAS  Google Scholar 

  34. Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM (2013) An extensive evaluation of read trimming effects on Illumina NGS data analysis

  35. Biesecker LG, Burke W, Kohane I, Plon SE, Zimmern R (2012) Next-generation sequencing in the clinic: are we ready? Nat Rev Genet 13:818–824

    Article  CAS  Google Scholar 

  36. Schuster SC (2007) Next-generation sequencing transforms today’s biology. Nature 200:16–18

    Google Scholar 

  37. Iyer MK, Chinnaiyan AM, Maher CA (2011) ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics 27:2903–2904

    Article  CAS  Google Scholar 

  38. Bansal V, Bafna V (2008) HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24:i153–i159

    Article  Google Scholar 

  39. Krueger F, Kreck B, Franke A, Andrews SR (2012) DNA methylome analysis using short bisulfite sequencing data. Nat Methods 9:145–151

    Article  CAS  Google Scholar 

  40. Wang X, Ghosh S, Guo S-W (2001) Quantitative quality control in microarray image processing and data acquisition. Nucl Acids Res 29:e75

    Article  CAS  Google Scholar 

  41. Miyazaki Y, Sunagawa M, Higashibata A, Ishioka N, Babasaki K, Yamazaki T (2010) Differentially expressed genes under simulated microgravity in fruiting bodies of the fungus Pleurotus ostreatus. FEMS Microbiol Lett 307:72–79

    Article  CAS  Google Scholar 

  42. Purevdorj-Gage B, Sheehan K, Hyman L (2006) Effects of low-shear modeled microgravity on cell function, gene expression, and phenotype in Saccharomyces cerevisiae. Appl Environ Microbiol 72:4569–4575

    Article  CAS  Google Scholar 

  43. Moreno-Vargas L, Correa-Basurto J, Maroun RC, Fernández FJ (2012) Homology modeling of the structure of acyl coA: isopenicillin N-acyltransferase (IAT) from Penicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking. J Mol Model 18:1189–1205

    Article  CAS  Google Scholar 

  44. Wilson JW, Ott CM, Ramamurthy R, Porwollik S, McClelland M, Pierson DL, Nickerson CA (2002) Low-shear modeled microgravity alters the Salmonella enterica serovar Typhimurium stress response in an RpoS-independent manner. Appl Environ Microbiol 68:5408–5416

    Article  CAS  Google Scholar 

  45. van den Berg MA, Albang R, Albermann K, Badger JH, Daran J-M, Driessen AJ, Garcia-Estrada C, Fedorova ND, Harris DM, Heijne WH (2008) Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol 26:1161–1168

    Article  CAS  Google Scholar 

  46. Pao SS, Paulsen IT, Saier MH (1998) Major facilitator superfamily. Microbiol Mol Biol Rev 62:1–34

    CAS  Google Scholar 

  47. Askew C, Sellam A, Epp E, Hogues H, Mullick A, Nantel A, Whiteway M (2009) Transcriptional regulation of carbohydrate metabolism in the human pathogen Candida albicans. PLoS Pathog 5:e1000612

    Article  CAS  Google Scholar 

  48. Freitas FZ, de Paula RM, Barbosa LCB, Terenzi HF, Bertolini MC (2010) cAMP signaling pathway controls glycogen metabolism in Neurospora crassa by regulating the glycogen synthase gene expression and phosphorylation. Fungal Genet Biol 47:43–52

    Article  CAS  Google Scholar 

  49. Boudreau BA, Larson TM, Brown DW, Busman M, Roberts ES, Kendra DF, McQuade KL (2013) Impact of temperature stress and validamycin A on compatible solutes and fumonisin production in F. verticillioides: role of trehalose-6-phosphate synthase. Fungal Genet Biol 57:1–10

    Article  CAS  Google Scholar 

  50. Foster AJ, Jenkinson JM, Talbot NJ (2003) Trehalose synthesis and metabolism are required at different stages of plant infection by Magnaporthe grisea. The EMBO Journal 22:225–235

    Article  CAS  Google Scholar 

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Acknowledgments

We would like to thank Genotypic technologies Pvt Limited for the NGS services. This research was supported by the National Research Foundation of Korea (NRF) Grant No. 1201002578 funded by the Korean Government and Sathish Kumar was supported by university research grants from the Chonbuk national university.

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Authors and Affiliations

  1. Department of Forest Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea

    Yesupatham Sathishkumar & Yang Soo Lee

  2. Department of Food Science and Technology, College of Agriculture and Life Sciences, Chonbuk National University, Jeonju, 561-756, Republic of Korea

    Chandran Krishnaraj

  3. Department of Biotechnology, Vels University, Chennai, 600117, India

    Kalyanaraman Rajagopal

  4. School of Biosciences and Technology, VIT University, Vellore, 632014, India

    Dwaipayan Sen

  5. Cellular and Molecular Therapeutics Laboratory, Centre for Biomaterials, Cellular and Molecular Theranostics, School of Biosciences and Technology, VIT University, Vellore, 632014, India

    Dwaipayan Sen

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  1. Yesupatham Sathishkumar
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Correspondence to Yang Soo Lee.

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Sathishkumar, Y., Krishnaraj, C., Rajagopal, K. et al. High throughput de novo RNA sequencing elucidates novel responses in Penicillium chrysogenum under microgravity. Bioprocess Biosyst Eng 39, 223–231 (2016). https://doi.org/10.1007/s00449-015-1506-4

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  • DOI: https://doi.org/10.1007/s00449-015-1506-4

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