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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

A comparison of the cre1 locus in Trichoderma reesei QM6a and RUT C30. The cre1 gene is located on scaffold 2. The respective location of the neighboring genes is also given. The cre1.1 mutation in RUT C30 comprises a region of 2478 bp, which is highlighted by a grey box. The two nucleotides given in grey could not be assigned unambiguously to one of the ends of the gap.
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Figure 4: A comparison of the cre1 locus in Trichoderma reesei QM6a and RUT C30. The cre1 gene is located on scaffold 2. The respective location of the neighboring genes is also given. The cre1.1 mutation in RUT C30 comprises a region of 2478 bp, which is highlighted by a grey box. The two nucleotides given in grey could not be assigned unambiguously to one of the ends of the gap.

Mentions: As the reason for this gene deletion in RUT C30 is unknown, we wondered whether it would be topologically related to the cre1.1 mutation. The cre1 locus in this strain has been shown to be truncated [11], but the exact length of the mutation and its genomic location has not yet been reported. A BLAST search of the H. jecorina genome sequence database with the cloned cre1 gene identified it to be located on scaffold 2: 786955–789433 (ID 120117), and thus distant from the locus of the lesion which was identified in this paper. In order to identify the cre1.1 mutation, we amplified and sequenced the cre1 locus in strain RUT C30. Using the primers Cre1fw and CreIIr (Table 1), PCR with QM9414 DNA resulted in a 3565 bp fragment as expected, whereas RUT C30 yielded a fragment of 1087 bp only. Sequencing of the fragment obtained with RUT C30, and its alignment with the sequence of scaffold 2 (Fig. 4) revealed the loss of a 2478 bp fragment which starts 3' of the region encoding the CRE1 zinc finger and reaches into a noncoding region. The coding region of the immediately following gene (tre12588) was not affected.


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)

A comparison of the cre1 locus in Trichoderma reesei QM6a and RUT C30. The cre1 gene is located on scaffold 2. The respective location of the neighboring genes is also given. The cre1.1 mutation in RUT C30 comprises a region of 2478 bp, which is highlighted by a grey box. The two nucleotides given in grey could not be assigned unambiguously to one of the ends of the gap.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: A comparison of the cre1 locus in Trichoderma reesei QM6a and RUT C30. The cre1 gene is located on scaffold 2. The respective location of the neighboring genes is also given. The cre1.1 mutation in RUT C30 comprises a region of 2478 bp, which is highlighted by a grey box. The two nucleotides given in grey could not be assigned unambiguously to one of the ends of the gap.
Mentions: As the reason for this gene deletion in RUT C30 is unknown, we wondered whether it would be topologically related to the cre1.1 mutation. The cre1 locus in this strain has been shown to be truncated [11], but the exact length of the mutation and its genomic location has not yet been reported. A BLAST search of the H. jecorina genome sequence database with the cloned cre1 gene identified it to be located on scaffold 2: 786955–789433 (ID 120117), and thus distant from the locus of the lesion which was identified in this paper. In order to identify the cre1.1 mutation, we amplified and sequenced the cre1 locus in strain RUT C30. Using the primers Cre1fw and CreIIr (Table 1), PCR with QM9414 DNA resulted in a 3565 bp fragment as expected, whereas RUT C30 yielded a fragment of 1087 bp only. Sequencing of the fragment obtained with RUT C30, and its alignment with the sequence of scaffold 2 (Fig. 4) revealed the loss of a 2478 bp fragment which starts 3' of the region encoding the CRE1 zinc finger and reaches into a noncoding region. The coding region of the immediately following gene (tre12588) was not affected.

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