Dataset Information

Whole Genome Metabolism - Verrucosispora maris (strain AB-18-032)

ABSTRACT:

Whole Genome Metabolism of "Verrucosispora maris (strain AB-18-032)"

This is a whole genome metabolism model of Verrucosispora maris (strain AB-18-032).

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: BMID000000140965 .

Other models with the same genus include BMID000000021798 BMID000000021799 BMID000000021800 BMID000000021801 BMID000000021802 BMID000000021803 BMID000000021804 BMID000000021805 BMID000000021806 BMID000000021807 BMID000000021808 BMID000000021809 BMID000000021810 BMID000000021811 BMID000000021812 BMID000000117605 BMID000000117606 BMID000000117607 BMID000000117608 BMID000000117609 BMID000000117610 BMID000000117611 BMID000000117612 BMID000000117613 BMID000000117614 BMID000000117615 BMID000000117616 BMID000000117617 BMID000000117618 BMID000000117619 BMID000000117620 BMID000000117621 BMID000000117622 BMID000000117623 BMID000000117624 BMID000000117625 BMID000000117626 BMID000000117627 BMID000000117628 BMID000000117629 BMID000000117630 BMID000000117631 BMID000000117632 BMID000000117633 BMID000000117634 BMID000000117635 BMID000000117636 BMID000000117637 BMID000000117638 BMID000000117639 BMID000000117640 BMID000000117641 BMID000000117642 BMID000000117643 BMID000000117644 BMID000000117645 BMID000000117646 BMID000000117647 BMID000000117648 BMID000000117649 BMID000000117650 BMID000000117651 BMID000000117652 BMID000000117653 BMID000000117654 BMID000000117655 BMID000000117656 BMID000000117657 BMID000000117658 BMID000000117659 BMID000000117660 BMID000000117661 BMID000000117662 BMID000000117663 BMID000000117664 BMID000000117665 BMID000000117666 BMID000000117667 BMID000000117668 BMID000000117669 BMID000000117670 BMID000000117671 BMID000000117672 BMID000000117673 BMID000000117674 BMID000000117675 BMID000000117676 BMID000000117677 BMID000000117678 BMID000000117679 BMID000000117680 BMID000000117681 BMID000000117682 BMID000000117683 BMID000000117684 BMID000000117685 BMID000000117686 BMID000000117687 BMID000000117688 BMID000000117689 BMID000000117690 BMID000000117691 BMID000000117692 BMID000000117693 BMID000000117694 BMID000000117695 .

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: BMID000000140965 | 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 - Verrucosispora maris (strain AB-18-032)

Publications

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

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