Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum
Open accessAbstract
Industrial penicillin production with the filamentous fungus Penicillium chrysogenum is based on an unprecedented effort in microbial strain improvement. To gain more insight into penicillin synthesis, we sequenced the 32.19 Mb genome of P. chrysogenum Wisconsin54-1255 and identified numerous genes responsible for key steps in penicillin production. DNA microarrays were used to compare the transcriptomes of the sequenced strain and a penicillinG high-producing strain, grown in the presence and absence of the side-chain precursor phenylacetic acid. Transcription of genes involved in biosynthesis of valine, cysteine and alpha-aminoadipic acid-precursors for penicillin biosynthesis-as well as of genes encoding microbody proteins, was increased in the high-producing strain. Some gene products were shown to be directly controlling beta-lactam output. Many key cellular transport processes involving penicillins and intermediates remain to be characterized at the molecular level. Genes predicted to encode transporters were strongly overrepresented among the genes transcriptionally upregulated under conditions that stimulate penicillinG production, illustrating potential for future genomics-driven metabolic engineering.
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The full genome sequenced strain of P. chrysogenum (Wisconsin 54-1255, derived from NRRL 1951) is P. rubens.
“the full genome sequenced strain of P. chrysogenum are re-identified as P. rubens”
From Fleming’s penicillin producing strain is not Penicillium chrysogenum but P. rubens (2011) · cites this paper as van den Berg et al. 2008
The Abstract and Methods identify Wisconsin 54-1255 as the P. chrysogenum strain whose genome was sequenced; the Abstract also says industrial strains derive from NRRL1951. Neither passage, nor the additional passages searched, says Wisconsin 54-1255 was re-identified as P. rubens. That central taxonomic claim is therefore unsupported by this source. (LLM, conf=0.86)
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Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus
Fedorova, N. D., Khaldi, N., Joardar, V. S., Maiti, R., Amedeo, P., Anderson, M. J., Crabtree, J., Silva, J. C., Badger, J. H., Albarraq, A., et al. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000046 · Cited by 508 · cited 1× · see citing works
“Similar genomic islands have been found in other fungal genome”
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Research works printed but not linked: 11
- P-value Frequency of occurence MIPS_categories P-value Frequency of occurence MIPS_categories P-value Frequency of occurence MIPS_categories P-value Frequency of occurence MIPS_categories P-value Frequency of occurence P-value Frequency of occurence P-value Frequency of occurence P-value Frequency of occurence 26 of 2,472 9 of 467 7 of 170 6 of 62 3 of 30 3 of 15 5 of 126 13 of 1,069 13 of 910 14 of 809 11 of 379 6 of 165 14 of 819 4 of 63 6 of 183 71 of 2,472 30 of 1,069 16 of 379 25 of 809 19 of 379 25 of 819 12 of 183 11 of 150 92 of 2,472 44 of 1,069 36 of 760 18 of 377 18 of 410 31 of 819 Pc21g21370; Pc21g21380; Pc21g21390 Pc22g14900 Pc12g05420; Pc12g08580; Pc18g02180 Pc20g03220; Pc20g07710; Pc20g10940 Pc21g14890; Pc22g05940; Pc23g00630 Pc12g02680; Pc20g00530; Pc20g03210 Pc12g04370; Pc22g16570; Pc13g07230 Pc22g13130; Pc22g15180; Pc13g08990 Pc20g02910; Pc21g18210; Pc22g19440 Pc22g00210; Pc22g23100; Pc22g23830 Pc20g00640; Pc20g07270; Pc13g05320 Pc13g05830; Pc16g12440; Pc21g05430 Pc12g12060; Pc13g02430; Pc13g10120 Pc13g15810; Pc22g11360; Pc22g18410 Pc22g20630; Pc22g22710; Pc22g23110 Pc18g02530; Pc22g16780; Pc22g22510 Pc16g06870; Pc18g01240; Pc22g06310 Pc22g13190; Pc22g05800; Pc18g01330 Pc12g09020; Pc12g09030; Pc12g09040 Pc16g01770; Pc21g14280 5,000 500 Expression value 12 Published online at http://www.nature.com/naturebiotechnology/ Reprints and permissions information is available online at http://npg.nature.com/ reprintsandpermissions/
- Hersbach, G.J.M., Van der Beek, C.P. & Van Dijck, P.W.M. The penicillins: properties, biosynthesis, and fermentation. in Biotechnology of Industrial Antibiotics. Drugs and the Pharmaceutical Sciences vol. 22 (ed.
- Fierro, F. et al. The penicillin biosynthetic gene cluster is amplified in tandem repeats linked by conserved hexanucleotide sequences. Proc. Natl. Acad. Sci. USA 92, 6200-6204 (1995).
- Elander, R. Strain improvement and preservation of beta-lactam producing microorgan- isms. in Antibiotics Containing the Beta-Lactam Structure I. (eds. Demain, A.L. & Solomon, N.) 97-146, (Springer-Verlag, New York, 1983).
- Malloch, D. The Trichomaceae: relationships with other Ascomycetes. in Advances in Penicillium and Aspergillus Systematics (eds. Samson, R.A. & Pitt, J.I.) 365-382, (Plenum Press, New York, 1985).
- Thon, M.R. et al. The role of transposable element clusters in genome evolution and loss of synteny in the rice blast fungus Magnaporthe oryzae. Genome Biol. 7, R16 (2006).
- Baerends, R.J. et al. Genome2D: a visualization tool for the rapid analysis of bacterial transcriptome data. Genome Biol. 5, R37 (2004).
- Kunau, W.-H. (ed.). Peroxisomes: morphology, function, biogenesis and disorders. Biochim. Biophys Acta 1763 (2006).
- Gordon, M., Pan, S.C., Virgona, A. & Numerof, P. Biosynthesis of penicillin. I. Role of phenylacetic acid. Science 118, 43 (1953).
- MacQueen, J. Some methods for classification and analysis of multivariate observa- tions. Proc. Fifth Berkeley Symp. Math. Stat. Probability 1, 281-297, (Univ. California Press, Berkeley, 1967).
- Xu, Z. et al. Genome physical mapping from large-insert clones by fingerprint analysis with capillary electrophoresis: a robust physical map of Penicillium chrysogenum. Nucleic Acids Res. 33, e50 (2005).
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Growing a circular economy with fungal biotechnology: a white paper
Meyer, V., Basenko, E. Y., Benz, J. P., Braus, G. H., Caddick, M. X., Csukai, M., de Vries, R. P., Endy, D., Frisvad, J. C., Gunde-Cimerman, N., et al. (2020) · Fungal Biology and Biotechnology · doi:10.1186/s40694-020-00095-z · Cited by 515 · see citing works
Fleming’s penicillin producing strain is not Penicillium chrysogenum but P. rubens
Houbraken, J., Frisvad, J. C., & Samson, R. A. (2011) · IMA Fungus · doi:10.5598/imafungus.2011.02.01.12 · Cited by 262 · see citing works
Oud, B., Maris, A. J. A., Daran, J.-M., & Pronk, J. T. (2012) · FEMS Yeast Research · doi:10.1111/j.1567-1364.2011.00776.x · Cited by 82 · see citing works
Self-citation
- Authors
- van den Berg, M. A., Albang, R., Albermann, K., Badger, J. H., Daran, J.-M., M Driessen, A. J., Garcia-Estrada, C., Fedorova, N. D., Harris, D. M., Heijne, W. H. M., Joardar, V., W Kiel, J. A. K., Kovalchuk, A., Martín, J. F., Nierman, W. C., Nijland, J. G., Pronk, J. T., Roubos, J. A., van der Klei, I. J., van Peij, N. N. M. E., Veenhuis, M., von Döhren, H., Wagner, C., Wortman, J., & Bovenberg, R. A. L.
- Affiliations
- Biomax Informatics (Germany) (DE)
- J. Craig Venter Institute (US)
- Delft University of Technology (NL)
- DSM (Netherlands) (NL)
- University of Groningen (NL)
- ORCID
- Venue
- Nature Biotechnology
- Published
- 2008-09-28
- Volume
- 26
- Issue
- 10
- Pages
- 1161-1168
- ISSN
- 0733-222X (ISSN-L)
- 1087-0156
- 1546-1696
- OpenAlex
- W2169105416
- Cited by
- 473
- References
- 1
- Citations by year
- 2026: 6 · 2025: 10 · 2024: 13 · 2023: 16 · 2022: 17 · 2021: 22 · 2020: 32 · 2019: 24 · 2018: 25 · 2017: 22 · 2016: 29 · 2015: 39 · 2014: 42 · 2013: 39 · 2012: 41
- FWCI
- 22.03
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature Biotechnology (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (publishedVersion, cc-by-nc-sa)
- Buleria (Universidad de León) (submittedVersion, cc-by-nc-sa)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion, cc-by-nc-sa)
- Funders
- European Commission
- Ministerie van Economische Zaken
- Nederlandse Organisatie voor Wetenschappelijk Onderzoek
- Topics
- Health Sciences › Medicine › Pharmacology › Microbial Natural Products and Biosynthesis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- Penicillium chrysogenum, penicillin biosynthesis, genome sequencing, phenylacetic acid, penicillin G, valine biosynthesis, cysteine biosynthesis, alpha-aminoadipic acid, metabolic engineering
- MeSH terms
- Base Sequence, Chromosome Mapping, Fungal Proteins, Molecular Sequence Data, Penicillin G, Penicillium chrysogenum, Transcription Factors, Genome, Fungal, Sequence Analysis, DNA
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