Dataset Information

Whole Genome Metabolism - Lawsonia intracellularis (strain PHE/MN1-00)

ABSTRACT:

Whole Genome Metabolism of "Lawsonia intracellularis (strain PHE/MN1-00)"

This is a whole genome metabolism model of Lawsonia intracellularis (strain PHE/MN1-00).

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: BMID000000141400 .

Other models with the same genus include BMID000000020871 BMID000000020872 BMID000000020873 BMID000000020874 BMID000000020875 BMID000000020876 BMID000000020877 BMID000000020878 BMID000000020879 BMID000000020880 BMID000000020881 BMID000000020882 BMID000000020883 BMID000000020884 BMID000000020885 BMID000000113516 BMID000000113517 BMID000000113518 BMID000000113519 BMID000000113520 BMID000000113521 BMID000000113522 BMID000000113523 BMID000000113524 BMID000000113525 BMID000000113526 BMID000000113527 BMID000000113528 BMID000000113529 BMID000000113530 BMID000000113531 BMID000000113532 BMID000000113533 BMID000000113534 BMID000000113535 BMID000000113536 BMID000000113537 BMID000000113538 BMID000000113539 BMID000000113540 BMID000000113541 BMID000000113542 BMID000000113543 BMID000000113544 BMID000000113545 BMID000000113546 BMID000000113547 BMID000000113548 BMID000000113549 BMID000000113550 BMID000000113551 BMID000000113552 BMID000000113553 BMID000000113554 BMID000000113555 BMID000000113556 BMID000000113557 BMID000000113558 BMID000000113559 BMID000000113560 BMID000000113561 BMID000000113562 BMID000000113563 BMID000000113564 BMID000000113565 BMID000000113566 BMID000000113567 BMID000000113568 BMID000000113569 BMID000000113570 BMID000000113571 BMID000000142106 .

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: BMID000000141400 | 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 - Lawsonia intracellularis (strain PHE/MN1-00)

Publications

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

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