Dataset Information

Whole Genome Metabolism - Desulfatibacillum alkenivorans (strain AK-01)

ABSTRACT:

Whole Genome Metabolism of "Desulfatibacillum alkenivorans (strain AK-01)"

This is a whole genome metabolism model of Desulfatibacillum alkenivorans (strain AK-01).

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: BMID000000140925 .

Other models with the same genus include BMID000000014532 BMID000000014533 BMID000000014534 BMID000000014535 BMID000000014536 BMID000000014537 BMID000000014538 BMID000000014539 BMID000000014540 BMID000000014541 BMID000000014542 BMID000000014543 BMID000000014544 BMID000000014545 BMID000000014546 BMID000000014547 BMID000000088138 BMID000000088139 BMID000000088140 BMID000000088141 BMID000000088142 BMID000000088143 BMID000000088144 BMID000000088145 BMID000000088146 BMID000000088147 BMID000000088148 BMID000000088149 BMID000000088150 BMID000000088151 BMID000000088152 BMID000000088153 BMID000000088154 BMID000000088155 BMID000000088156 BMID000000088157 BMID000000088158 BMID000000088159 BMID000000088160 BMID000000088161 BMID000000088162 BMID000000088163 BMID000000088164 BMID000000088165 BMID000000088166 BMID000000088167 BMID000000088168 BMID000000088169 BMID000000088170 BMID000000088171 BMID000000088172 BMID000000088173 BMID000000088174 BMID000000088175 BMID000000088176 BMID000000088177 BMID000000088178 BMID000000088179 BMID000000088180 BMID000000088181 BMID000000088182 BMID000000088183 BMID000000088184 BMID000000088185 BMID000000088186 BMID000000088187 BMID000000088188 BMID000000088189 BMID000000088190 BMID000000088191 BMID000000088192 BMID000000088193 BMID000000088194 BMID000000088195 BMID000000088196 BMID000000088197 BMID000000088198 BMID000000088199 BMID000000088200 BMID000000088201 BMID000000088202 BMID000000088203 BMID000000088204 BMID000000088205 BMID000000088206 BMID000000088207 BMID000000088208 BMID000000088209 BMID000000088210 BMID000000088211 BMID000000088212 BMID000000088213 BMID000000088214 BMID000000088215 BMID000000088216 BMID000000088217 BMID000000088218 .

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: BMID000000140925 | 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 - Desulfatibacillum alkenivorans (strain AK-01)

Publications

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

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