Dataset Information

Whole Genome Metabolism - Thermosynechococcus elongatus (strain BP-1)

ABSTRACT:

Whole Genome Metabolism of "Thermosynechococcus elongatus (strain BP-1)"

This is a whole genome metabolism model of Thermosynechococcus elongatus (strain BP-1).

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: BMID000000140975 .

Other models with the same genus include BMID000000015245 BMID000000015246 BMID000000015247 BMID000000015248 BMID000000015249 BMID000000015250 BMID000000015251 BMID000000015252 BMID000000015253 BMID000000015254 BMID000000015255 BMID000000015256 BMID000000015257 BMID000000091333 BMID000000091334 BMID000000091335 BMID000000091336 BMID000000091337 BMID000000091338 BMID000000091339 BMID000000091340 BMID000000091341 BMID000000091342 BMID000000091343 BMID000000091344 BMID000000091345 BMID000000091346 BMID000000091347 BMID000000091348 BMID000000091349 BMID000000091350 BMID000000091351 BMID000000091352 BMID000000091353 BMID000000091354 BMID000000091355 BMID000000091356 BMID000000091357 BMID000000091358 BMID000000091359 BMID000000091360 BMID000000091361 BMID000000091362 BMID000000091363 BMID000000091364 BMID000000091365 BMID000000091366 BMID000000091367 BMID000000091368 BMID000000091369 BMID000000091370 BMID000000091371 BMID000000091372 BMID000000091373 BMID000000091374 BMID000000091375 BMID000000091376 BMID000000091377 BMID000000091378 BMID000000091379 BMID000000091380 BMID000000091381 BMID000000091382 BMID000000091383 BMID000000091384 BMID000000091385 BMID000000091386 BMID000000091387 BMID000000091388 BMID000000091389 BMID000000091390 BMID000000091391 BMID000000091392 BMID000000091393 BMID000000091394 BMID000000091395 BMID000000091396 BMID000000091397 BMID000000091398 BMID000000091399 BMID000000091400 BMID000000091401 BMID000000091402 BMID000000091403 BMID000000091404 BMID000000091405 BMID000000091406 BMID000000091407 BMID000000091408 .

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: BMID000000140975 | 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 - Thermosynechococcus elongatus (strain BP-1)

Publications

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

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