Dataset Information

Whole Genome Metabolism - Schizophyllum commune (strain H4-8 / FGSC 9210)

ABSTRACT:

Whole Genome Metabolism of "Schizophyllum commune (strain H4-8 / FGSC 9210)"

This is a whole genome metabolism model of Schizophyllum commune (strain H4-8 / FGSC 9210).

This model has been automatically generated by the SuBliMinaL Toolbox and libAnnotationSBML using information coming from from KEGG (release 66, April 2013, accessed via the resource's web services interface) and, where relevant, augmented with metabolic pathway information extracted from MetaCyc (version 17.0, March 2013).

This model has been produced by the path2models project and is currently hosted on BioModels Database and identified by: BMID000000140610 .

Other models with the same genus include BMID000000018864 BMID000000018865 BMID000000018866 BMID000000018867 BMID000000018868 BMID000000018869 BMID000000018870 BMID000000018871 BMID000000018872 BMID000000018873 BMID000000018874 BMID000000018875 BMID000000018876 BMID000000018877 BMID000000018878 BMID000000018879 BMID000000018880 BMID000000018881 BMID000000018882 BMID000000018883 BMID000000018884 BMID000000018885 BMID000000018886 BMID000000018887 BMID000000018888 BMID000000018889 BMID000000018890 BMID000000018891 BMID000000018892 BMID000000018893 BMID000000018894 BMID000000104858 BMID000000104859 BMID000000104860 BMID000000104861 BMID000000104862 BMID000000104863 BMID000000104864 BMID000000104865 BMID000000104866 BMID000000104867 BMID000000104868 BMID000000104869 BMID000000104870 BMID000000104871 BMID000000104872 BMID000000104873 BMID000000104874 BMID000000104875 BMID000000104876 BMID000000104877 BMID000000104878 BMID000000104879 BMID000000104880 BMID000000104881 BMID000000104882 BMID000000104883 BMID000000104884 BMID000000104885 BMID000000104886 BMID000000104887 BMID000000104888 BMID000000104889 BMID000000104890 BMID000000104891 BMID000000104892 BMID000000104893 BMID000000104894 BMID000000104895 BMID000000104896 BMID000000104897 BMID000000104898 BMID000000104899 BMID000000104900 BMID000000104901 BMID000000104902 BMID000000104903 BMID000000104904 BMID000000104905 BMID000000104906 BMID000000104907 BMID000000104908 BMID000000104909 BMID000000104910 BMID000000104911 BMID000000104912 BMID000000104913 BMID000000104914 BMID000000104915 BMID000000104916 BMID000000104917 BMID000000104918 BMID000000104919 BMID000000104920 BMID000000104921 BMID000000104922 BMID000000104923 BMID000000104924 BMID000000104925 BMID000000104926 BMID000000104927 BMID000000104928 BMID000000104929 .

To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

SUBMITTER: Path2Models project

PROVIDER: BMID000000140610 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel Finja F Rodriguez Nicolas N Swainston Neil N Wrzodek Clemens C Wrzodek Clemens C Czauderna Tobias T Keller Roland R Mittag Florian F Schubert Michael M Glont Mihai M Golebiewski Martin M van Iersel Martijn M Keating Sarah S Rall Matthias M Wybrow Michael M Hermjakob Henning H Hucka Michael M Kell Douglas B DB Müller Wolfgang W Mendes Pedro P Zell Andreas A Chaouiya Claudine C Saez-Rodriguez Julio J Schreiber Falk F Laibe Camille C Dräger Andreas A Le Novère Nicolas N

BMC systems biology 20131101

<h4>Background</h4>Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.<h4>Results</h4>To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources ...[more]

PMID: 24180668

Publication: 1/2

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Project description:tRNAs are encoded by a large gene family, usually with several isogenic tRNAs interacting with the same codon. Mutations in the anticodon region of other tRNAs can overcome specific tRNA deficiencies. Phylogenetic analysis suggests that such mutations have occurred in evolution, but the driving force is unclear. We show that in yeast suppressor mutations in other tRNAs are able to overcome deficiency of the essential TRT2-encoded tRNAThrCGU at high temperature (40°C). Surprisingly, these tRNA suppressor mutations were obtained after whole-genome transformation with DNA from thermotolerant Kluyveromyces marxianus or Ogataea polymorpha strains, but from which the mutations did apparently not originate. We suggest that transient presence of donor DNA in the host facilitates proliferation at high temperature and thus increases the chances for occurrence of spontaneous mutations suppressing defective growth at high temperature. Whole-genome sequence analysis of three transformants revealed only four to five non-synonymous mutations of which one causing TRT2 anticodon stem stabilization and two anticodon mutations in non-threonyl-tRNAs, tRNALysCUU and tRNAeMetCAU, were causative. Both anticodon mutations suppressed lethality of TRT2 deletion and apparently caused the respective tRNAs to become novel substrates for threonyl-tRNA synthetase. LC-MS/MS data could not detect any significant mistranslation and RT-qPCR results contradicted induction of the unfolded protein response. We suggest that stress conditions have been a driving force in evolution for the selection of anticodon-switching mutations in tRNAs as revealed by phylogenetic analysis. Importance of the work In this work we have identified for the first time the causative elements in a eukaryotic organism introduced by applying whole-genome transformation and responsible for the selectable trait of interest, i.e. high temperature tolerance. Surprisingly, the whole-genome transformants contained just a few SNPs, which were unrelated to the sequence of the donor DNA. In each of three independent transformants, we have identified a SNP in a tRNA, either stabilizing the essential tRNAThrCGU at high temperature or switching the anticodon of tRNALysCUU or tRNAeMetCAU into CGU, which is apparently enough for in vivo recognition by threonyl-tRNA synthetase. LC-MS/MS analysis indeed indicated absence of significant mistranslation. Phylogenetic analysis showed that similar mutations have occurred throughout evolution and we suggest that stress conditions may have been a driving force for their selection. The low number of SNPs introduced by whole-genome transformation may favor its application for improvement of industrial yeast strains.

Dataset Information

Whole Genome Metabolism - Schizophyllum commune (strain H4-8 / FGSC 9210)

Publications

Path2Models: large-scale generation of computational models from biochemical pathway maps.

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