Dataset Information

Whole Genome Metabolism - Methanoregula boonei (strain 6A8)

ABSTRACT:

Whole Genome Metabolism of "Methanoregula boonei (strain 6A8)"

This is a whole genome metabolism model of Methanoregula boonei (strain 6A8).

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: BMID000000141248 .

Other models with the same genus include BMID000000013774 BMID000000013775 BMID000000013776 BMID000000013777 BMID000000013778 BMID000000013779 BMID000000013780 BMID000000013781 BMID000000013782 BMID000000013783 BMID000000013784 BMID000000013785 BMID000000013786 BMID000000013787 BMID000000013788 BMID000000013789 BMID000000013790 BMID000000013791 BMID000000084839 BMID000000084840 BMID000000084841 BMID000000084842 BMID000000084843 BMID000000084844 BMID000000084845 BMID000000084846 BMID000000084847 BMID000000084848 BMID000000084849 BMID000000084850 BMID000000084851 BMID000000084852 BMID000000084853 BMID000000084854 BMID000000084855 BMID000000084856 BMID000000084857 BMID000000084858 BMID000000084859 BMID000000084860 BMID000000084861 BMID000000084862 BMID000000084863 BMID000000084864 BMID000000084865 BMID000000084866 BMID000000084867 BMID000000084868 BMID000000084869 BMID000000084870 BMID000000084871 BMID000000084872 BMID000000084873 BMID000000084874 BMID000000084875 BMID000000084876 BMID000000084877 BMID000000084878 BMID000000084879 BMID000000084880 BMID000000084881 BMID000000084882 BMID000000084883 BMID000000084884 BMID000000084885 BMID000000084886 BMID000000084887 BMID000000084888 BMID000000084889 BMID000000084890 BMID000000084891 BMID000000084892 BMID000000084893 BMID000000084894 BMID000000142471 .

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: BMID000000141248 | 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

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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 - Methanoregula boonei (strain 6A8)

Publications

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

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