Dataset Information

Whole Genome Metabolism - Thiomonas intermedia (strain K12)

ABSTRACT:

Whole Genome Metabolism of "Thiomonas intermedia (strain K12)"

This is a whole genome metabolism model of Thiomonas intermedia (strain K12).

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: BMID000000141524 .

Other models with the same genus include BMID000000005290 BMID000000005291 BMID000000005292 BMID000000005293 BMID000000005294 BMID000000005295 BMID000000005296 BMID000000005297 BMID000000005298 BMID000000005299 BMID000000005300 BMID000000005301 BMID000000005302 BMID000000005303 BMID000000005304 BMID000000005305 BMID000000049079 BMID000000049080 BMID000000049081 BMID000000049082 BMID000000049083 BMID000000049084 BMID000000049085 BMID000000049086 BMID000000049087 BMID000000049088 BMID000000049089 BMID000000049090 BMID000000049091 BMID000000049092 BMID000000049093 BMID000000049094 BMID000000049095 BMID000000049096 BMID000000049097 BMID000000049098 BMID000000049099 BMID000000049100 BMID000000049101 BMID000000049102 BMID000000049103 BMID000000049104 BMID000000049105 BMID000000049106 BMID000000049107 BMID000000049108 BMID000000049109 BMID000000049110 BMID000000049111 BMID000000049112 BMID000000049113 BMID000000049114 BMID000000049115 BMID000000049116 BMID000000049117 BMID000000049118 BMID000000049119 BMID000000049120 BMID000000049121 BMID000000049122 BMID000000049123 BMID000000049124 BMID000000049125 BMID000000049126 BMID000000049127 BMID000000049128 BMID000000049129 BMID000000049130 BMID000000049131 BMID000000049132 BMID000000049133 BMID000000049134 BMID000000049135 BMID000000049136 BMID000000049137 BMID000000049138 BMID000000049139 BMID000000049140 BMID000000049141 BMID000000049142 BMID000000049143 BMID000000049144 BMID000000049145 BMID000000049146 BMID000000049147 BMID000000049148 BMID000000049149 BMID000000049150 BMID000000049151 BMID000000049152 BMID000000049153 BMID000000049154 BMID000000049155 BMID000000049156 BMID000000049157 BMID000000049158 BMID000000049159 BMID000000049160 BMID000000049161 BMID000000142146 .

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: BMID000000141524 | 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 - Thiomonas intermedia (strain K12)

Publications

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

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