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The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome.

Seidl V, Gamauf C, Druzhinina IS, Seiboth B, Hartl L, Kubicek CP - BMC Genomics (2008)

Bottom Line: The mutation of the cre1 locus has specifically occurred in RUT C30.Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on alpha-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.Our data place a general caveat on the use of H. jecorina RUT C30 for further basic research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166-5, A-1060 Wien, Austria. vseidl@mail.zserv.tuwien.ac.at

ABSTRACT

Background: The hypercellulolytic mutant Hypocrea jecorina (anamorph Trichoderma reesei) RUT C30 is the H. jecorina strain most frequently used for cellulase fermentations and has also often been employed for basic research on cellulase regulation. This strain has been reported to contain a truncated carbon catabolite repressor gene cre1 and is consequently carbon catabolite derepressed. To date this and an additional frame-shift mutation in the glycoprotein-processing beta-glucosidase II encoding gene are the only known genetic differences in strain RUT C30.

Results: In the present paper we show that H. jecorina RUT C30 lacks an 85 kb genomic fragment, and consequently misses additional 29 genes comprising transcription factors, enzymes of the primary metabolism and transport proteins. This loss is already present in the ancestor of RUT C30--NG 14--and seems to have occurred in a palindromic AT-rich repeat (PATRR) typically inducing chromosomal translocations, and is not linked to the cre1 locus. The mutation of the cre1 locus has specifically occurred in RUT C30. Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on alpha-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.

Conclusion: Our data place a general caveat on the use of H. jecorina RUT C30 for further basic research.

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Related in: MedlinePlus

Phenotype array analysis of carbon source profiles of H. jecorina QM6a (Q)and RUT C30 (R). Only carbon sources where a difference to the parent strain QM6a was found are shown, and given in a color code. The OD750 refers to measurements at 48 hrs of growth, at which time the value is proportional to the growth rate (OD750/h) of the fungus on the respective carbon source. Carbon sources which are highlighted by a grey background are those which result in higher growth rates in RUT C30.
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Figure 6: Phenotype array analysis of carbon source profiles of H. jecorina QM6a (Q)and RUT C30 (R). Only carbon sources where a difference to the parent strain QM6a was found are shown, and given in a color code. The OD750 refers to measurements at 48 hrs of growth, at which time the value is proportional to the growth rate (OD750/h) of the fungus on the respective carbon source. Carbon sources which are highlighted by a grey background are those which result in higher growth rates in RUT C30.

Mentions: In view of the relatively strong abundance of metabolic genes in the genomic region which is missing in H. jecorina RUT C30, we performed a comprehensive analysis of its ability to assimilate (i.e. grow on) carbon sources using 95 carbon sources contained in the Biolog Phenotype Microarrays, and compared it to its wild-type strain QM6a. The data obtained (Fig. 6) identified several striking differences: strain RUT C30 had a strongly impaired growth on L-arabinose, L-erythritol, D-galactose and also 2-keto-D-gluconic acid. Interestingly, the opposite effect (= an enhancement of the assimilation rate) was also observed with some other carbon sources, e.g. glycerol, N-acetyl-β-D-glucosamine, D-mannitol, D-fructose, D-trehalose, D-mannose, D-ribose). This strongly reduced growth on L-arabinose, L-erythritol and also D-galactose suggested to us that one of the aldo/keto-reductases identified as lacking in strain RUT C30 (i.e. ID 65142, ID 6567, and ID 64956) could be involved in polyol assimilation. In order to test this hypothesis, we prepared cell free extracts from strains QM9414 and RUT C30, and tested these activities in cell-free extracts. As shown Table 3, both strains of H. jecorina had high NAD+-linked dehydrogenase activities with xylitol, L-arabinitol and erythritol and NADPH-linked dehydrogenase activities with D-xylose and L-arabinose as substrates, respectively. Activities with the other coenzyme (i.e. NADP with xylitol, L-arabinitol and erythritol; and NADH with D-xylose and L-arabinose) were negligible, with the exception of some NADP+-linked activity of strain RUT C30 on xylitol, which was absent from strain QM9414. In general, activities in strain RUT C30 were significantly higher. Only the NAD+-linked erythritol dehydrogenase activity was similar in both strains. These data indicate that the loss of the three aldo/ketoreductases in RUT C30 has apparently no effect on its metabolism of the major polyols and therefore cannot explain the different growth pattern of strain RUT C30 on L-arabinose and L-erythritol


The Hypocrea jecorina (Trichoderma reesei) hypercellulolytic mutant RUT C30 lacks a 85 kb (29 gene-encoding) region of the wild-type genome.

Seidl V, Gamauf C, Druzhinina IS, Seiboth B, Hartl L, Kubicek CP - BMC Genomics (2008)

Phenotype array analysis of carbon source profiles of H. jecorina QM6a (Q)and RUT C30 (R). Only carbon sources where a difference to the parent strain QM6a was found are shown, and given in a color code. The OD750 refers to measurements at 48 hrs of growth, at which time the value is proportional to the growth rate (OD750/h) of the fungus on the respective carbon source. Carbon sources which are highlighted by a grey background are those which result in higher growth rates in RUT C30.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2483294&req=5

Figure 6: Phenotype array analysis of carbon source profiles of H. jecorina QM6a (Q)and RUT C30 (R). Only carbon sources where a difference to the parent strain QM6a was found are shown, and given in a color code. The OD750 refers to measurements at 48 hrs of growth, at which time the value is proportional to the growth rate (OD750/h) of the fungus on the respective carbon source. Carbon sources which are highlighted by a grey background are those which result in higher growth rates in RUT C30.
Mentions: In view of the relatively strong abundance of metabolic genes in the genomic region which is missing in H. jecorina RUT C30, we performed a comprehensive analysis of its ability to assimilate (i.e. grow on) carbon sources using 95 carbon sources contained in the Biolog Phenotype Microarrays, and compared it to its wild-type strain QM6a. The data obtained (Fig. 6) identified several striking differences: strain RUT C30 had a strongly impaired growth on L-arabinose, L-erythritol, D-galactose and also 2-keto-D-gluconic acid. Interestingly, the opposite effect (= an enhancement of the assimilation rate) was also observed with some other carbon sources, e.g. glycerol, N-acetyl-β-D-glucosamine, D-mannitol, D-fructose, D-trehalose, D-mannose, D-ribose). This strongly reduced growth on L-arabinose, L-erythritol and also D-galactose suggested to us that one of the aldo/keto-reductases identified as lacking in strain RUT C30 (i.e. ID 65142, ID 6567, and ID 64956) could be involved in polyol assimilation. In order to test this hypothesis, we prepared cell free extracts from strains QM9414 and RUT C30, and tested these activities in cell-free extracts. As shown Table 3, both strains of H. jecorina had high NAD+-linked dehydrogenase activities with xylitol, L-arabinitol and erythritol and NADPH-linked dehydrogenase activities with D-xylose and L-arabinose as substrates, respectively. Activities with the other coenzyme (i.e. NADP with xylitol, L-arabinitol and erythritol; and NADH with D-xylose and L-arabinose) were negligible, with the exception of some NADP+-linked activity of strain RUT C30 on xylitol, which was absent from strain QM9414. In general, activities in strain RUT C30 were significantly higher. Only the NAD+-linked erythritol dehydrogenase activity was similar in both strains. These data indicate that the loss of the three aldo/ketoreductases in RUT C30 has apparently no effect on its metabolism of the major polyols and therefore cannot explain the different growth pattern of strain RUT C30 on L-arabinose and L-erythritol

Bottom Line: The mutation of the cre1 locus has specifically occurred in RUT C30.Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on alpha-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.Our data place a general caveat on the use of H. jecorina RUT C30 for further basic research.

View Article: PubMed Central - HTML - PubMed

Affiliation: Research Area Gene Technology and Applied Biochemistry, Institute of Chemical Engineering, Vienna University of Technology, Getreidemarkt 9/166-5, A-1060 Wien, Austria. vseidl@mail.zserv.tuwien.ac.at

ABSTRACT

Background: The hypercellulolytic mutant Hypocrea jecorina (anamorph Trichoderma reesei) RUT C30 is the H. jecorina strain most frequently used for cellulase fermentations and has also often been employed for basic research on cellulase regulation. This strain has been reported to contain a truncated carbon catabolite repressor gene cre1 and is consequently carbon catabolite derepressed. To date this and an additional frame-shift mutation in the glycoprotein-processing beta-glucosidase II encoding gene are the only known genetic differences in strain RUT C30.

Results: In the present paper we show that H. jecorina RUT C30 lacks an 85 kb genomic fragment, and consequently misses additional 29 genes comprising transcription factors, enzymes of the primary metabolism and transport proteins. This loss is already present in the ancestor of RUT C30--NG 14--and seems to have occurred in a palindromic AT-rich repeat (PATRR) typically inducing chromosomal translocations, and is not linked to the cre1 locus. The mutation of the cre1 locus has specifically occurred in RUT C30. Some of the genes that are lacking in RUT C30 could be correlated with pronounced alterations in its phenotype, such as poor growth on alpha-linked oligo- and polyglucosides (loss of maltose permease), or disturbance of osmotic homeostasis.

Conclusion: Our data place a general caveat on the use of H. jecorina RUT C30 for further basic research.

Show MeSH
Related in: MedlinePlus