Genomic mutational analysis of the impact of the classical strain improvement program on β-lactam producing Penicillium chrysogenum

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Salo, Oleksandr V ^a   Ries, Marco ^b,c   Medema, Marnix H ^d   Lankhorst, Peter P ^e   Vreeken, Rob J ^b,c   Bovenberg, Roel A L ^a,e   Driessen, Arnold J M ^a,f  

^a UNIVERSITY OF GRONINGEN   (Netherlands)

^b LEIDEN UNIVERSITY   (Netherlands)

^c LEIDEN UNIVERSITY   (Netherlands)

^d WAGENINGEN UNIVERSITY   (Netherlands)

^e DSM RESOLVE   (Netherlands)

^f Kluyver Center for Genomics of Industrial Fermentation   (Netherlands)

Author keywords

Penicillium chrysogenum; Polyketide synthases; Secondary metabolism; Sequencing; Sorbicillinoids

Indexed keywords

BETA LACTAM DERIVATIVE; BISORBICILLINOL; BISVERTINOLON; CHRYSOGINE; CHRYSOGINE B; CHRYSOGINE C; DIHYDROBISVERTINOLONE; DIHYDROSORBICILLINOL; FUNGISPORIN; GLANDICOLINE A; HISTIDYLTRYPTOPHANYLDIKETOPIPERZINE; MELEAGIN; N PYROVOYLANTHRANILAMID; NEOXALINE; NONRIBOSOMAL PEPTIDE SYNTHETASE; OXOSORBICILLINOL; PENICILLIN DERIVATIVE; PENICILLIN G; PENICILLIN K; PENICILLIN V; POLYKETIDE SYNTHASE; ROQUEFORTINE C; ROQUEFORTINE D; ROQUEFORTINE F; ROQUEFORTINE M; ROQUEFORTINE N; SORBICILLINOID; SORBICILLINOL; TETRAHYDROBISVERTINOLONE; UNCLASSIFIED DRUG; UNINDEXED DRUG; BETA LACTAM;

ARTICLE; CLASSICAL STRAIN IMPROVEMENT; COMPARATIVE STUDY; CONTROLLED STUDY; DRUG SYNTHESIS; FUNGAL GENOME; FUNGAL METABOLISM; FUNGAL STRAIN; GENE CLUSTER; GENE EXPRESSION; GENE MUTATION; GENE SEQUENCE; GENETIC STRAIN; METABOLITE; MUTATIONAL ANALYSIS; NONHUMAN; PENICILLIUM CHRYSOGENUM; SECONDARY METABOLISM; FUNGAL GENE; GENETICS; METABOLISM; METABOLOME; MULTIGENE FAMILY; MUTATION; SPECIES DIFFERENCE;

BETA-LACTAMS; GENES, FUNGAL; METABOLOME; MULTIGENE FAMILY; MUTATION; PENICILLIUM CHRYSOGENUM; SPECIES SPECIFICITY;

EID: 84963545878     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2154-4     Document Type: Article

References (31)

1. Backus MP, Stauffer JF. The production and selection of a family of strains in Penicillium chrysogenum. Mycologia. 1955;47(4):429-63.
2. van den Berg MA, Albang R, Albermann K, Badger JH, Daran JM, Driessen AJ, et al. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat Biotechnol. 2008;26(10):1161-8.
3. Hoff B, Kamerewerd J, Sigl C, Mitterbauer R, Zadra I, Kurnsteiner H, et al. Two components of a velvet-like complex control hyphal morphogenesis, conidiophore development, and penicillin biosynthesis in Penicillium chrysogenum. Eukaryot Cell. 2010;9(8):1236-50.
4. Jami MS, Barreiro C, Garcia-Estrada C, Martin JF. Proteome analysis of the penicillin producer Penicillium chrysogenum: characterization of protein changes during the industrial strain improvement. Mol Cell Proteomics. 2010;9(6):1182-98.
5. Kiel JA, van den Berg MA, Fusetti F, Poolman B, Bovenberg RA, Veenhuis M, et al. Matching the proteome to the genome: the microbody of penicillinproducing Penicillium chrysogenum cells. Funct Integr Genomics. 2009;9(2):167-84.
6. Kopke K, Hoff B, Bloemendal S, Katschorowski A, Kamerewerd J, Kuck U. Members of the Penicillium chrysogenum velvet complex play functionally opposing roles in the regulation of penicillin biosynthesis and conidiation. Eukaryot Cell. 2013;12(2):299-310.
7. Veiga T, Nijland JG, Driessen AJ, Bovenberg RA, Touw H, van den Berg MA, et al. Impact of velvet complex on transcriptome and penicillin G production in glucose-limited chemostat cultures of a beta-lactam high-producing Penicillium chrysogenum strain. Omics. 2012;16(6):320-33.
8. Newbert RW, Barton B, Greaves P, Harper J, Turner G. Analysis of a commercially improved Penicillium chrysogenum strain series: involvement of recombinogenic regions in amplification and deletion of the penicillin biosynthesis gene cluster. J Ind Microbiol Biotechnol. 1997;19(1):18-27.
9. Ries MI, Ali H, Lankhorst PP, Hankemeier T, Bovenberg RA, Driessen AJ, et al. Novel key metabolites reveal further branching of the roquefortine/meleagrin biosynthetic pathway. J Biol Chem. 2013;288(52):37289-95.
10. Garcia-Estrada C, Ullan RV, Albillos SM, Fernandez-Bodega MA, Durek P, von Dohren H, et al. A single cluster of coregulated genes encodes the biosynthesis of the mycotoxins roquefortine C and meleagrin in Penicillium chrysogenum. Chem Biol. 2011;18(11):1499-512.
11. Ali H, Ries MI, Nijland JG, Lankhorst PP, Hankemeier T, Bovenberg RA, et al. A branched biosynthetic pathway is involved in production of roquefortine and related compounds in Penicillium chrysogenum. PLoS One. 2013;8(6), e65328.
12. Ali H, Ries MI, Lankhorst PP, van der Hoeven RA, Schouten OL, Noga M, et al. A non-canonical NRPS is involved in the synthesis of fungisporin and related hydrophobic cyclic tetrapeptides in Penicillium chrysogenum. PLoS One. 2014;9(6), e98212.
13. Cram DJ, Tishler M. Mold metabolites; isolation of several compounds from clinical penicillin. J Am Chem Soc. 1948;70(12):4238.
14. Maskey RP, Grun-Wollny I, Laatsch H. Sorbicillin analogues and related dimeric compounds from Penicillium notatum. J Nat Prod. 2005;68(6):865-70.
15. Abe N, Yamamoto K, Hirota A. Novel fungal metabolites, demethylsorbicillin and oxosorbicillinol, isolated from Trichoderma sp. USF-2690. Biosci Biotechnol Biochem. 2000;64(3):620-2.
16. Reategui RF, Wicklow DT, Gloer JB. Phaeofurans and sorbicillin analogues from a fungicolous Phaeoacremonium species (NRRL 32148). J Nat Prod. 2006;69(1):113-7.
17. Sindi SS, Onal S, Peng LC, Wu HT, Raphael BJ. An integrative probabilistic model for identification of structural variation in sequencing data. Genome Biol. 2012;13(3):R22.
18. Kanehisa M, Goto S, Hattori M, Aoki-Kinoshita KF, Itoh M, Kawashima S, et al. From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 2006;34(Database issue):D354-357.
19. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, et al. The COG database: an updated version includes eukaryotes. BMC Bioinformatics. 2003;4(1471-2105 (Electronic)):41.
20. Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28(1):33-6.
21. Weber T, Blin K, Duddela S, Krug D, Kim HU, Bruccoleri R, et al. antiSMASH 3.0-a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43(W1):W237-243.
22. Puel O, Galtier P, Oswald IP. Biosynthesis and toxicological effects of patulin. Toxins. 2010;2(4):613-31.
23. Aa F, Abood A, Fisch KM, Osipow A, Davison J, Avramovic M, et al. Oxidative dearomatisation: the key step of sorbicillinoid biosynthesis. Chemical Science. 2014;5(2):523-7.
24. Abe N, Arakawa T, Yamamoto K, Hirota A. Biosynthesis of bisorbicillinoid in Trichoderma sp. USF-2690; evidence for the biosynthetic pathway, via sorbicillinol, of sorbicillin, bisorbicillinol, bisorbibutenolide, and bisorbicillinolide. Biosci Biotechnol Biochem. 2002;66(10):2090-9.
25. Bayram O, Krappmann S, Ni M, Bok JW, Helmstaedt K, Valerius O, et al. VelB/VeA/LaeA complex coordinates light signal with fungal development and secondary metabolism. Science. 2008;320(5882):1504-6.
26. Kosalkova K, Garcia-Estrada C, Ullan RV, Godio RP, Feltrer R, Teijeira F, et al. The global regulator LaeA controls penicillin biosynthesis, pigmentation and sporulation, but not roquefortine C synthesis in Penicillium chrysogenum. Biochimie. 2009;91(2):214-25.
27. Specht T, Dahlmann TA, Zadra I, Kurnsteiner H, Kuck U: Complete Sequencing and Chromosome-Scale Genome Assembly of the Industrial Progenitor Strain P2niaD18 from the Penicillin Producer Penicillium chrysogenum. Genome Announce 2014, 2(4). doi: 10.1128/genomeA.00577-14.
28. Harris DM, van der Krogt ZA, Klaassen P, Raamsdonk LM, Hage S, van den Berg MA, et al. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genomics. 2009;10:75.
29. Bringmann G, Lang G, Gulder TAM, Tsuruta H, Muhlbacher J, Maksimenka K, et al. The first sorbicillinoid alkaloids, the antileukemic sorbicillactones A and B, from a sponge-derived Penicillium chrysogenum strain. Tetrahedron. 2005;61(30):7252-65.
30. Kovalchuk A, Weber SS, Nijland JG, Bovenberg RA, Driessen AJ. Fungal ABC transporter deletion and localization analysis. Methods Mol Biol. 2012;835:1-16.
31. Nijland JG, Ebbendorf B, Woszczynska M, Boer R, Bovenberg RA, Driessen AJ. Nonlinear biosynthetic gene cluster dose effect on penicillin production by Penicillium chrysogenum. Appl Environ Microbiol. 2010;76(21):7109-15.