International Space Station conditions alter genomics, proteomics, and metabolomics in Aspergillus nidulans
The first global genomic, proteomic, and secondary metabolomic characterization of the filamentous fungus Aspergillus nidulans following growth onboard the International Space Station (ISS) is reported. The investigation included the A. nidulans wild-type and three mutant strains, two of which were genetically engineered to enhance secondary metabolite production. Whole genome sequencing revealed that ISS conditions altered the A. nidulans genome in specific regions. In strain CW12001, which features overexpression of the secondary metabolite global regulator laeA, ISS conditions induced the loss of the laeA stop codon. Differential expression of proteins involved in stress response, carbohydrate metabolic processes, and secondary metabolite biosynthesis was also observed. ISS conditions significantly decreased prenyl xanthone production in the wild-type strain and increased asperthecin production in LO1362 and CW12001, which are deficient in a major DNA repair mechanism. These data provide valuable insights into the adaptation mechanism of A. nidulans to spacecraft environments.
KeywordsAspergillus nidulans International Space Station Genomics Proteomics Metabolomics
Part of the research described in this publication was carried out at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with NASA. We would like to thank astronauts Tim Peake, Tim Kopra, and Jeff Williams for handling the samples aboard the ISS, the Implementation Team at NASA Ames Research Center, and BioServe Space Technologies for coordinating this effort. © 2018 California Institute of Technology. Government sponsorship acknowledged.
Reference herein to any specific commercial product, process, or service by trade name, trademark, manufacturer, or otherwise does not constitute or imply its endorsement by the U.S. Government or the Jet Propulsion Laboratory, California Institute of Technology.
JR drafted the manuscript, contributed to sample processing, and was responsible for data analysis and interpretation. AB contributed to sample processing and data interpretation. AC and MK conducted protein sample processing, LC/MS analyses, and proteome data processing. YC contributed to secondary metabolic analysis and interpretation. SM contributed to variant analysis. JY generated the CW12001 strain. SC was responsible for sample integration into flight hardware. FK was responsible for project implementation and generating metadata from the ISS. JS contributed to genome data processing and variant analysis. KV and CW designed the study, interpreted the data, and drafted the manuscript. All authors read and approved the final manuscript.
This research was funded by a 2012 Space Biology NNH12ZTT001N grant nos. 19-12829-26 under Task Order NNN13D111T awarded to CW and KV, which also funded JR and AB.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- Andersen MR, Nielsen JB, Klitgaard A, Petersen LM, Zachariasen M, Hansen TJ, Blicher LH, Gotfredsen CH, Larsen T, Nielsen KF, Mortensen UH (2013) Accurate prediction of secondary metabolite gene clusters in filamentous fungi. Proc Natl Acad Sci 110:E99–E107. https://doi.org/10.1073/pnas.1205532110 CrossRefGoogle Scholar
- Andrews S (2010) FastQC: a quality control tool for high throughput sequence dataGoogle Scholar
- Arnaud MB, Chibucos MC, Costanzo MC, Crabtree J, Inglis DO, Lotia A, Orvis J, Shah P, Skrzypek MS, Binkley G, Miyasato SR, Wortman JR, Sherlock G (2010) The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community. Nucleic Acids Res 38:D420–D427. https://doi.org/10.1093/nar/gkp751 CrossRefGoogle Scholar
- Bayram ÖS, Bayram Ö, Valerius O, Park HS, Irniger S, Gerke J, Ni M, Han K-H, Yu J-H, Braus GH (2010) LaeA control of velvet family regulatory proteins for light-dependent development and fungal cell-type specificity. PLoS Genet 6:e1001226. https://doi.org/10.1371/journal.pgen.1001226 CrossRefGoogle Scholar
- Chang P-K, Scharfenstein LL, Ehrlich KC, Wei Q, Bhatnagar D, Ingber BF (2012) Effects of laeA deletion on Aspergillus flavus conidial development and hydrophobicity may contribute to loss of aflatoxin production. Fungal Biol 116:298–307. https://doi.org/10.1016/j.funbio.2011.12.003 CrossRefGoogle Scholar
- Checinska A, Probst AJ, Vaishampayan P, White JR, Kumar D, Stepanov VG, Fox GE, Nilsson HR, Pierson DL, Perry J, Venkateswaran K (2015) Microbiomes of the dust particles collected from the International Space Station and Spacecraft Assembly Facilities. Microbiome 3:50. https://doi.org/10.1186/s40168-015-0116-3 CrossRefGoogle Scholar
- Chiang Y-M, Szewczyk E, Nayak T, Davidson AD, Sanchez JF, Lo H-C, Ho W-Y, Simityan H, Kuo E, Praseuth A, Watanabe K, Oakley BR, Wang CCC (2008) Molecular genetic mining of the Aspergillus secondary metabolome: discovery of the emericellamide biosynthetic pathway. Chem Biol 15:527–532. https://doi.org/10.1016/j.chembiol.2008.05.010 CrossRefGoogle Scholar
- Council NR (2011) Recapturing a future for space exploration: life and physical sciences research for a new eraGoogle Scholar
- DePristo MA, Banks E, Poplin RE, Garimella KV, Maguire JR, Hartl C, Philippakis AA, del Angel G, Rivas M, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43:491–498. https://doi.org/10.1038/ng.806 CrossRefGoogle Scholar
- Fujii K, Kurata H, Odashima S, Hatsuda Y (1976) Tumor induction by a single subcutaneous injection of sterigmatocystin in newborn mice. Cancer Res 36:1615–1618Google Scholar
- Galagan JE, Calvo SE, Cuomo C, Ma L-J, Wortman JR, Batzoglou S, Lee S-I, Baştürkmen M, Spevak CC, Clutterbuck J, Kapitonov V, Jurka J, Scazzocchio C, Farman M, Butler J, Purcell S, Harris S, Braus GH, Draht O, Busch S, D’Enfert C, Bouchier C, Goldman GH, Bell-Pedersen D, Griffiths-Jones S, Doonan JH, Yu J, Vienken K, Pain A, Freitag M, Selker EU, Archer DB, Peñalva MA, Oakley BR, Momany M, Tanaka T, Kumagai T, Asai K, Machida M, Nierman WC, Denning DW, Caddick M, Hynes M, Paoletti M, Fischer R, Miller B, Dyer P, Sachs MS, Osmani SA, Birren BW (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438:1105–1115. https://doi.org/10.1038/nature04341 CrossRefGoogle Scholar
- Guo J, Han N, Zhang Y, Wang H, Zhang X, Su L, Liu C, Li J, Chen C, Liu C (2015) Use of genome sequencing to assess nucleotide structure variation of Staphylococcus aureus strains cultured in spaceflight on Shenzhou-X, under simulated microgravity and on the ground. Microbiol Res 170:61–68. https://doi.org/10.1016/j.micres.2014.09.001 CrossRefGoogle Scholar
- Knox BP, Blachowicz A, Palmer JM, Romsdahl J, Huttenlocher A, Wang CCC, Keller NP, Venkateswaran K (2016) Characterization of Aspergillus fumigatus isolates from air and surfaces of the International Space Station. mSphere 1:e00227–e00216. https://doi.org/10.1128/mSphere.00227-16 CrossRefGoogle Scholar
- Kosalková K, García-Estrada C, Ullán RV, Godio RP, Feltrer R, Teijeira F, Mauriz E, Martín JF (2009) The global regulator LaeA controls penicillin biosynthesis, pigmentation and sporulation, but not roquefortine C synthesis in Penicillium chrysogenum. Biochimie 91:214–225. https://doi.org/10.1016/j.biochi.2008.09.004 CrossRefGoogle Scholar
- de la Torre Noetzel R, Miller AZ, de la Rosa JM, Pacelli C, Onofri S, García Sancho L, Cubero B, Lorek A, Wolter D, de Vera JP (2018) Cellular responses of the lichen Circinaria gyrosa in Mars-like conditions. Front Microbiol 9. https://doi.org/10.3389/fmicb.2018.00308
- Lo H-C, Entwistle R, Guo C-J, Ahuja M, Szewczyk E, Hung J-H, Chiang Y-M, Oakley BR, Wang CCC (2012) Two separate gene clusters encode the biosynthetic pathway for the meroterpenoids austinol and dehydroaustinol in Aspergillus nidulans. J Am Chem Soc 134:4709–4720. https://doi.org/10.1021/ja209809t CrossRefGoogle Scholar
- Mora M, Perras A, Alekhova TA, Wink L, Krause R, Aleksandrova A, Novozhilova T, Moissl-Eichinger C (2016) Resilient microorganisms in dust samples of the International Space Station—survival of the adaptation specialists. Microbiome 4:65. https://doi.org/10.1186/s40168-016-0217-7 CrossRefGoogle Scholar
- Oakley CE, Ahuja M, Sun W-W, Entwistle R, Akashi T, Yaegashi J, Guo C-J, Cerqueira GC, Russo Wortman J, Wang CCC, Chiang Y-M, Oakley BR (2017) Discovery of McrA, a master regulator of Aspergillus secondary metabolism. Mol Microbiol 103:347–365. https://doi.org/10.1111/mmi.13562 CrossRefGoogle Scholar
- Onofri S, Selbmann L, Pacelli C, de Vera JP, Horneck G, Hallsworth JE, Zucconi L (2018a) Integrity of the DNA and cellular ultrastructure of cryptoendolithic fungi in space or Mars conditions: a 1.5-year study at the International Space Station. Life Basel Switz 8:. https://doi.org/10.3390/life8020023
- Onofri S, Selbmann L, Pacelli C, Zucconi L, Rabbow E, de Vera J-P (2018b) Survival, DNA, and ultrastructural integrity of a cryptoendolithic Antarctic fungus in Mars and lunar rock analogues exposed outside the International Space Station. Astrobiology. https://doi.org/10.1089/ast.2017.1728
- Pierson DL (2001) Microbial contamination of spacecraft. Gravit Space Biol Bull 14:1–6Google Scholar
- Plubell DL, Wilmarth PA, Zhao Y, Fenton AM, Minnier J, Reddy AP, Klimek J, Yang X, David LL, Pamir N (2017) Extended multiplexing of tandem mass tags (TMT) labeling reveals age and high fat diet specific proteome changes in mouse epididymal adipose tissue. Mol Cell Proteomics 16:873–890. https://doi.org/10.1074/mcp.M116.065524 CrossRefGoogle Scholar
- Pusztahelyi T, Klement É, Szajli E, Klem J, Miskei M, Karányi Z, Emri T, Kovács S, Orosz G, Kovács KL, Medzihradszky KF, Prade RA, Pócsi I (2011) Comparison of transcriptional and translational changes caused by long-term menadione exposure in Aspergillus nidulans. Fungal Genet Biol 48:92–103. https://doi.org/10.1016/j.fgb.2010.08.006 CrossRefGoogle Scholar
- Tixador R, Richoilley G, Gasset G, Templier J, Bes J, Moatti N, Lapchine L (1985) Study of minimal inhibitory concentration of antibiotics on bacteria cultivated in vitro in space (Cytos 2 experiment). Aviat Space Environ Med 56:748–751Google Scholar
- Tkavc R, Matrosova VY, Grichenko OE, Gostinčar C, Volpe RP, Klimenkova P, Gaidamakova EK, Zhou CE, Stewart BJ, Lyman MG, Malfatti SA, Rubinfeld B, Courtot M, Singh J, Dalgard CL, Hamilton T, Frey KG, Gunde-Cimerman N, Dugan L, Daly MJ (2018) Prospects for fungal bioremediation of acidic radioactive waste sites: characterization and genome sequence of Rhodotorula taiwanensis MD1149. Front Microbiol 8. https://doi.org/10.3389/fmicb.2017.02528
- Wilson JW, Ott CM, Quick L, Davis R, zu Bentrup KH, Crabbé A, Richter E, Sarker S, Barrila J, Porwollik S, Cheng P, McClelland M, Tsaprailis G, Radabaugh T, Hunt A, Shah M, Nelman-Gonzalez M, Hing S, Parra M, Dumars P, Norwood K, Bober R, Devich J, Ruggles A, CdeBaca A, Narayan S, Benjamin J, Goulart C, Rupert M, Catella L, Schurr MJ, Buchanan K, Morici L, McCracken J, Porter MD, Pierson DL, Smith SM, Mergeay M, Leys N, Stefanyshyn-Piper HM, Gorie D, Nickerson CA (2008) Media ion composition controls regulatory and virulence response of Salmonella in spaceflight. PLoS One 3:e3923. https://doi.org/10.1371/journal.pone.0003923 CrossRefGoogle Scholar
- Yaegashi J, Oakley BR, Wang CCC (2014) Recent advances in genome mining of secondary metabolite biosynthetic gene clusters and the development of heterologous expression systems in Aspergillus nidulans. J Ind Microbiol Biotechnol 41:433–442. https://doi.org/10.1007/s10295-013-1386-z CrossRefGoogle Scholar