Dataset Information

Whole Genome Metabolism - Sinorhizobium meliloti (strain AK83)

ABSTRACT:

Whole Genome Metabolism of "Sinorhizobium meliloti (strain AK83)"

This is a whole genome metabolism model of Sinorhizobium meliloti (strain AK83).

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: BMID000000140734 .

Other models with the same genus include BMID000000001789 BMID000000001790 BMID000000001791 BMID000000001792 BMID000000001793 BMID000000001794 BMID000000001795 BMID000000001796 BMID000000001797 BMID000000001798 BMID000000001799 BMID000000001800 BMID000000001801 BMID000000001802 BMID000000001803 BMID000000001804 BMID000000001805 BMID000000035436 BMID000000035437 BMID000000035438 BMID000000035439 BMID000000035440 BMID000000035441 BMID000000035442 BMID000000035443 BMID000000035444 BMID000000035445 BMID000000035446 BMID000000035447 BMID000000035448 BMID000000035449 BMID000000035450 BMID000000035451 BMID000000035452 BMID000000035453 BMID000000035454 BMID000000035455 BMID000000035456 BMID000000035457 BMID000000035458 BMID000000035459 BMID000000035460 BMID000000035461 BMID000000035462 BMID000000035463 BMID000000035464 BMID000000035465 BMID000000035466 BMID000000035467 BMID000000035468 BMID000000035469 BMID000000035470 BMID000000035471 BMID000000035472 BMID000000035473 BMID000000035474 BMID000000035475 BMID000000035476 BMID000000035477 BMID000000035478 BMID000000035479 BMID000000035480 BMID000000035481 BMID000000035482 BMID000000035483 BMID000000035484 BMID000000035485 BMID000000035486 BMID000000035487 BMID000000035488 BMID000000035489 BMID000000035490 BMID000000035491 BMID000000035492 BMID000000035493 BMID000000035494 BMID000000035495 BMID000000035496 BMID000000035497 BMID000000035498 BMID000000035499 BMID000000035500 BMID000000035501 BMID000000035502 BMID000000035503 BMID000000035504 BMID000000035505 BMID000000035506 BMID000000035507 BMID000000035508 BMID000000035509 BMID000000035510 BMID000000035511 BMID000000035512 BMID000000035513 BMID000000035514 BMID000000035515 BMID000000035516 BMID000000035517 BMID000000035518 BMID000000035519 BMID000000035520 BMID000000035521 BMID000000035522 BMID000000035523 BMID000000035524 BMID000000141224 BMID000000021403 BMID000000021404 BMID000000021405 BMID000000021406 BMID000000021407 BMID000000021408 BMID000000021409 BMID000000021410 BMID000000021411 BMID000000021412 BMID000000021413 BMID000000021414 BMID000000021415 BMID000000021416 BMID000000021417 BMID000000021418 BMID000000021419 BMID000000116024 BMID000000116025 BMID000000116026 BMID000000116027 BMID000000116028 BMID000000116029 BMID000000116030 BMID000000116031 BMID000000116032 BMID000000116033 BMID000000116034 BMID000000116035 BMID000000116036 BMID000000116037 BMID000000116038 BMID000000116039 BMID000000116040 BMID000000116041 BMID000000116042 BMID000000116043 BMID000000116044 BMID000000116045 BMID000000116046 BMID000000116047 BMID000000116048 BMID000000116049 BMID000000116050 BMID000000116051 BMID000000116052 BMID000000116053 BMID000000116054 BMID000000116055 BMID000000116056 BMID000000116057 BMID000000116058 BMID000000116059 BMID000000116060 BMID000000116061 BMID000000116062 BMID000000116063 BMID000000116064 BMID000000116065 BMID000000116066 BMID000000116067 BMID000000116068 BMID000000116069 BMID000000116070 BMID000000116071 BMID000000116072 BMID000000116073 BMID000000116074 BMID000000116075 BMID000000116076 BMID000000116077 BMID000000116078 BMID000000116079 BMID000000116080 BMID000000116081 BMID000000116082 BMID000000116083 BMID000000116084 BMID000000116085 BMID000000116086 BMID000000116087 BMID000000116088 BMID000000116089 BMID000000116090 BMID000000116091 BMID000000116092 BMID000000116093 BMID000000116094 BMID000000116095 BMID000000116096 BMID000000116097 BMID000000116098 BMID000000116099 BMID000000116100 BMID000000116101 BMID000000116102 BMID000000116103 BMID000000116104 BMID000000116105 BMID000000116106 BMID000000116107 BMID000000142118 BMID000000142230 BMID000000142285 BMID000000142306 BMID000000142672 BMID000000142806 .

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: BMID000000140734 | 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 - Sinorhizobium meliloti (strain AK83)

Publications

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

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