Dataset Information

Whole Genome Metabolism - Myxococcus xanthus (strain DK 1622)

ABSTRACT:

Whole Genome Metabolism of "Myxococcus xanthus (strain DK 1622)"

This is a whole genome metabolism model of Myxococcus xanthus (strain DK 1622).

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: BMID000000140860 .

Other models with the same genus include BMID000000022399 BMID000000022400 BMID000000022401 BMID000000022402 BMID000000022403 BMID000000022404 BMID000000022405 BMID000000022406 BMID000000022407 BMID000000022408 BMID000000022409 BMID000000022410 BMID000000022411 BMID000000022412 BMID000000022413 BMID000000022414 BMID000000120354 BMID000000120355 BMID000000120356 BMID000000120357 BMID000000120358 BMID000000120359 BMID000000120360 BMID000000120361 BMID000000120362 BMID000000120363 BMID000000120364 BMID000000120365 BMID000000120366 BMID000000120367 BMID000000120368 BMID000000120369 BMID000000120370 BMID000000120371 BMID000000120372 BMID000000120373 BMID000000120374 BMID000000120375 BMID000000120376 BMID000000120377 BMID000000120378 BMID000000120379 BMID000000120380 BMID000000120381 BMID000000120382 BMID000000120383 BMID000000120384 BMID000000120385 BMID000000120386 BMID000000120387 BMID000000120388 BMID000000120389 BMID000000120390 BMID000000120391 BMID000000120392 BMID000000120393 BMID000000120394 BMID000000120395 BMID000000120396 BMID000000120397 BMID000000120398 BMID000000120399 BMID000000120400 BMID000000120401 BMID000000120402 BMID000000120403 BMID000000120404 BMID000000120405 BMID000000120406 BMID000000120407 BMID000000120408 BMID000000120409 BMID000000120410 BMID000000120411 BMID000000120412 BMID000000120413 BMID000000120414 BMID000000120415 BMID000000120416 BMID000000120417 BMID000000120418 BMID000000120419 BMID000000120420 BMID000000120421 BMID000000120422 BMID000000120423 BMID000000120424 BMID000000120425 BMID000000120426 BMID000000120427 BMID000000120428 BMID000000120429 BMID000000120430 BMID000000120431 BMID000000120432 BMID000000120433 BMID000000120434 BMID000000120435 BMID000000120436 BMID000000120437 BMID000000120438 BMID000000120439 BMID000000120440 BMID000000142005 BMID000000142476 .

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: BMID000000140860 | 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 - Myxococcus xanthus (strain DK 1622)

Publications

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

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