Dataset Information

Whole Genome Metabolism - Cenarchaeum symbiosum (strain A)

ABSTRACT:

Whole Genome Metabolism of "Cenarchaeum symbiosum (strain A)"

This is a whole genome metabolism model of Cenarchaeum symbiosum (strain A).

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: BMID000000141317 .

Other models with the same genus include BMID000000016725 BMID000000016726 BMID000000016727 BMID000000016728 BMID000000016729 BMID000000016730 BMID000000016731 BMID000000016732 BMID000000016733 BMID000000016734 BMID000000016735 BMID000000016736 BMID000000016737 BMID000000016738 BMID000000016739 BMID000000096984 BMID000000096985 BMID000000096986 BMID000000096987 BMID000000096988 BMID000000096989 BMID000000096990 BMID000000096991 BMID000000096992 BMID000000096993 BMID000000096994 BMID000000096995 BMID000000096996 BMID000000096997 BMID000000096998 BMID000000096999 BMID000000097000 BMID000000097001 BMID000000097002 BMID000000097003 BMID000000097004 BMID000000097005 BMID000000097006 BMID000000097007 BMID000000097008 BMID000000097009 BMID000000097010 BMID000000097011 BMID000000097012 BMID000000097013 BMID000000097014 BMID000000097015 BMID000000097016 BMID000000097017 BMID000000097018 BMID000000097019 BMID000000097020 BMID000000097021 BMID000000097022 BMID000000097023 BMID000000097024 BMID000000097025 BMID000000097026 BMID000000097027 BMID000000097028 BMID000000097029 BMID000000097030 BMID000000097031 BMID000000097032 BMID000000097033 BMID000000097034 BMID000000097035 BMID000000097036 BMID000000097037 BMID000000097038 BMID000000097039 BMID000000097040 .

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: BMID000000141317 | 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 - Cenarchaeum symbiosum (strain A)

Publications

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

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