Dataset Information

Whole Genome Metabolism - Acidianus hospitalis (strain W1)

ABSTRACT:

Whole Genome Metabolism of "Acidianus hospitalis (strain W1)"

This is a whole genome metabolism model of Acidianus hospitalis (strain W1).

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: BMID000000141911 .

Other models with the same genus include BMID000000026888 BMID000000026889 BMID000000026890 BMID000000026891 BMID000000026892 BMID000000026893 BMID000000026894 BMID000000026895 BMID000000026896 BMID000000026897 BMID000000026898 BMID000000026899 BMID000000026900 BMID000000026901 BMID000000026902 BMID000000138432 BMID000000138433 BMID000000138434 BMID000000138435 BMID000000138436 BMID000000138437 BMID000000138438 BMID000000138439 BMID000000138440 BMID000000138441 BMID000000138442 BMID000000138443 BMID000000138444 BMID000000138445 BMID000000138446 BMID000000138447 BMID000000138448 BMID000000138449 BMID000000138450 BMID000000138451 BMID000000138452 BMID000000138453 BMID000000138454 BMID000000138455 BMID000000138456 BMID000000138457 BMID000000138458 BMID000000138459 BMID000000138460 BMID000000138461 BMID000000138462 BMID000000138463 BMID000000138464 BMID000000138465 BMID000000138466 BMID000000138467 BMID000000138468 BMID000000138469 BMID000000138470 BMID000000138471 BMID000000138472 BMID000000138473 BMID000000138474 BMID000000138475 BMID000000138476 BMID000000138477 BMID000000138478 BMID000000138479 BMID000000138480 BMID000000138481 BMID000000138482 BMID000000138483 BMID000000138484 BMID000000138485 BMID000000138486 BMID000000138487 BMID000000138488 BMID000000138489 BMID000000138490 BMID000000138491 BMID000000138492 BMID000000138493 BMID000000138494 .

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: BMID000000141911 | 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 - Acidianus hospitalis (strain W1)

Publications

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

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