Construction of an hdfA Penicillium chrysogenum strain impaired in non-homologous end-joining and analysis of its potential for functional analysis studies

Fungal Genetics and Biology

Volumn 46, Issue 5, 2009, Pages 418-426

  Snoek, I S I ^a,b   van der Krogt, Z A ^a,b   Touw, H ^c   Kerkman, R ^c   Pronk, J T ^a,b   Bovenberg, R A L ^c   van den Berg, M A ^c   Daran, J M ^a,b  

^a DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

^c DSM RESOLVE   (Netherlands)

Author keywords

Beta lactams; Functional analysis; hdfA; Homologous recombination; Ku70 homolog; Penicillium chrysogenum; Targeting efficiency

Indexed keywords

GLUCOSE; PENICILLIN G; TRANSCRIPTOME;

ARTICLE; CONTROLLED STUDY; FUNGAL GENE; FUNGAL STRAIN; GENE DELETION; GENE TARGETING; HDFA GENE; HDFB GENE; NONHUMAN; PENICILLIUM CHRYSOGENUM; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; RNA ANALYSIS;

ANIMALS; DNA REPAIR ENZYMES; FUNGAL PROTEINS; GENE DELETION; GENE TARGETING; MOLECULAR BIOLOGY; PENICILLIUM CHRYSOGENUM; RECOMBINATION, GENETIC;

FUNGI; PENICILLIUM CHRYSOGENUM;

EID: 64049104778     PISSN: 10871845     EISSN: 10960937     Source Type: Journal    
DOI: 10.1016/j.fgb.2009.02.008     Document Type: Article

References (37)

1. Baganz F., Hayes A., Marren D., Gardner D.J., and Oliver S.G. Suitability of replacement markers for functional analysis studies in Saccharomyces cerevisiae. Yeast 13 (1997) 1563-1573
2. Baganz F., Hayes A., Farquhar R., Butler P.R., Gardner D.C., and Oliver S.G. Quantitative analysis of yeast gene function using competition experiments in continuous culture. Yeast 14 (1998) 1417-1427
3. Button D.K. Biochemical basis for whole-cell uptake kinetics: specific affinity, oligotrophic capacity, and the meaning of the Michaelis constant. Appl. Environ. Microbiol. 57 (1991) 2033-2038
4. Casqueiro J., Gutierrez S., Banuelos O., Hijarrubia M.J., and Martin J.F. Gene targeting in Penicillium chrysogenum: disruption of the lys2 gene leads to penicillin overproduction. J. Bacteriol. 181 (1999) 1181-1188
5. Chang P.K. A highly efficient gene-targeting system for Aspergillus parasiticus. Lett. Appl. Microbiol. 46 (2008) 587-592
6. de Laat, W.T.A.M., Preusting, J.C.G., Koekman, B.P., 2002. Fermentative production of valuable compounds on an industrial scale using chemically defined media. International Patent Application WO0039758
7. Dekker, P.J.T., van den Berg, M.A., 2005. Filamentous fungal cells with improved homologous recombination efficiency. International Patent Application WO05095624.
8. Fierro F., Kosalková K., utiérrez S., and artin J.F. Autonomously replicating plasmids carrying the AMA1 region in Penicillium chrysogenum. Curr. Genet. 29 (1996) 482-489
9. Haarmann T., Lorenz N., and Tudzynski P. Use of a nonhomologous end joining deficient strain (Deltaku70) of the ergot fungus Claviceps purpurea for identification of a nonribosomal peptide synthetase gene involved in ergotamine biosynthesis. Fungal Genet. Biol. 45 (2007) 35-44
10. Harder W., and Kuenen J.G. A review. Microbial selection in continuous culture. J. Appl. Bacteriol. 43 (1977) 1-24
11. Harris D.M., Diderich J.A., van der Krogt Z.A., Luttik M.A., Raamsdonk L.M., Bovenberg R.A., van Gulik W.M., van Dijken J.P., and Pronk J.T. Enzymic analysis of NADPH metabolism in beta-lactam-producing Penicillium chrysogenum: presence of a mitochondrial NADPH dehydrogenase. Metab. Eng. 8 (2006) 91-101
12. Harris D.M., van der Krogt Z.A., Klaassen P., Raamsdonk L.M., Hage S., van den Berg M.A., Bovenberg R.A., Pronk J.T., and Daran J.M. Exploring and dissecting genome-wide gene expression responses of Penicillium chrysogenum to phenylacetic acid consumption and penicillinG production. BMC Genom. 10 (2009) 75 10.1186/1471-2164-10-75
13. Harris D.M., Westerlaken I., Schipper D., van der Krogt Z.A., Gombert A.K., Sutherland J., Raamsdonk L.M., van den Berg M.A., Bovenberg R.A.L., Pronk J.T., and Daran J.M. Engineering of Penicillium chrysogenum for fermentative production of a novel carbamoylated cephem antibiotic precursor. Metab. Eng. 11 (2009) 125-137
14. Ishibashi K., Suzuki K., Ando Y., Takakura C., and Inoue H. Nonhomologous chromosomal integration of foreign DNA is completely dependent on MUS-53 (humanLig4homolog) in Neurospora. Proc. Natl. Acad. Sci. USA 103 (2006) 14871-14876
15. Kiel J.A., van der Klei I.J., van den Berg M.A., Bovenberg R.A., and Veenhuis M. Overproduction of a single protein, Pc-Pex11p, results in 2-fold enhanced penicillin production by Penicillium chrysogenum. Fungal Genet. Biol. 42 (2005) 154-164
16. Kooistra R., Hooykaas P.J., and Steensma H.Y. Efficient gene targeting in Kluyveromyces lactis. Yeast 21 (2004) 781-792
17. Krappmann S., Sasse C., and Braus G.H. Gene targeting in Aspergillus fumigatus by homologous recombination is facilitated in a nonhomologous end- joining-deficient genetic background. Eukaryot. Cell 5 (2006) 212-215
18. Kuenen J.G., and Beudeker R.F. Microbiology of thiobacilli and other sulphur-oxidizing autotrophs, mixotrophs and heterotrophs. Philos. Trans. Roy. Soc. Lond. B. Biol. Sci. 298 (1982) 473-497
19. Maruyama J., and Kitamoto K. Multiple gene disruptions by marker recycling with highly efficient gene-targeting background (DeltaligD) in Aspergillus oryzae. Biotechnol. Lett. 30 (2008) 1811-1817
20. Meyer V., Arentshorst M., El-Ghezal A., Drews A.C., Kooistra R., van den Hondel C.A., and Ram A.F. Highly efficient gene targeting in the Aspergillus niger kusA mutant. J. Biotechnol. 128 (2007) 770-775
21. Monod J. Recherche sur la croissance des cultures bacteriennes (1942), Hermann et Cie, Paris
22. Nayak T., Szewczyk E., Oakley C.E., Osmani A., Ukil L., Murray S.L., Osmani S.A., and Oakley B.R. A versatile and efficient gene-targeting system for Aspergillus nidulans. Genetics 172 (2006) 1557-1566
23. Nielsen J.B., Nielsen M.L., and Mortensen U.H. Transient disruption of non-homologous end-joining facilitates targeted genome manipulations in the filamentous fungus Aspergillus nidulans. Fungal Genet. Biol. 45 (2008) 165-170
24. Ninomiya Y., Suzuki K., Ishii C., and Inoue H. Highly efficient gene replacements in Neurospora strains deficient for nonhomologous end-joining. Proc. Natl. Acad. Sci. USA 101 (2004) 12248-12253
25. Pastwa E., and Blasiak J. Non-homologous DNA end joining. Acta Biochim. Polym. 50 (2003) 891-908
26. Postma E., Verduyn C., Scheffers W.A., and van Dijken J.P. Enzymic analysis of the Crabtree effect in glucose-limited chemostat cultures of Saccharomyces cerevisiae. Appl. Environ. Microbiol. 55 (1989) 468-477
27. Ramakers C., Ruijter J.M., Deprez R.H., and Moorman A.F. Assumption-free analysis of quantitative real-time polymerase chain reaction (PCR) data. Neurosci. Lett. 339 (2003) 62-66
28. Robin J., Jakobsen M., Beyer M., Noorman H., and Nielsen J. Physiological characterisation of Penicillium chrysogenum strains expressing the expandase gene from Streptomyces clavuligerus during batch cultivations. Growth and adipoyl-7-aminodeacetoxycephalosporanic acid production. Appl. Microbiol. Biotechnol. 57 (2001) 357-362
29. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
30. Swinkels, B.W., Selten, G.C.M., Bakhuis, J.G., Bovenberg, R.A.L., Vollebregt, A.W., 1997. The use of homologous amdS genes as selectable markers. International Patent Application WO9706261.
31. Tai S.L., Snoek I.S.I., Luttik M.A., Almering M.J., Walsh M.C., Pronk J.T., and Daran J.M. Correlation between transcript profiles and fitness of deletion mutants in anaerobic chemostat cultures of Saccharomyces cerevisiae. Microbiology 153 (2007) 877-886
32. Takahashi T., Masuda T., and Koyama Y. Enhanced gene targeting frequency in ku70 and ku80 disruption mutants of Aspergillus sojae and Aspergillus oryzae. Mol. Genet. Genom. 275 (2006) 460-470
33. Thykaer J., and Nielsen J. Metabolic engineering of beta-lactam production. Metab. Eng. 5 (2003) 56-69
34. Tusher V.G., Tibshirani R., and Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA 98 (2001) 5116-5121
35. van den Berg, M.A., Bovenberg, R.A.L., Raamsdonk, L.M., Sutherland, J.D., de Vroom, E., Vollinga, R.C.R., 2004. Cephem Compound International Patent Application WO04106347.
36. van den Berg M.A., Westerlaken I., Leeflang C., Kerkman R., and Bovenberg R.A.L. Functional characterization of the penicillin biosynthetic gene cluster of Penicillium chrysogenum Wisconsin 54-1255. Fungal Genet. Biol. 44 (2007) 830-844
37. van den Berg M.A., Albang R., Albermann K., Badger J.H., Daran J.M., Driessen A.J., Garcia-Estrada C., Fedorova N.D., Harris D.M., Heijne W.H., Joardar V., Kiel J.A., 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., Veenhuis M., von Döhren H., Wagner C., Wortman J., and Bovenberg R.A. Genome sequencing and analysis of the filamentous fungus Penicillium chrysogenum. Nat. Biotechnol. 26 (2008) 1161-1168