Dataset Information

Whole Genome Metabolism - Orientia tsutsugamushi (strain Ikeda)

ABSTRACT:

Whole Genome Metabolism of "Orientia tsutsugamushi (strain Ikeda)"

This is a whole genome metabolism model of Orientia tsutsugamushi (strain Ikeda).

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: BMID000000141817 .

Other models with the same genus include BMID000000011781 BMID000000011782 BMID000000011783 BMID000000011784 BMID000000011785 BMID000000011786 BMID000000011787 BMID000000011788 BMID000000011789 BMID000000011790 BMID000000011791 BMID000000011792 BMID000000077145 BMID000000077146 BMID000000077147 BMID000000077148 BMID000000077149 BMID000000077150 BMID000000077151 BMID000000077152 BMID000000077153 BMID000000077154 BMID000000077155 BMID000000077156 BMID000000077157 BMID000000077158 BMID000000077159 BMID000000077160 BMID000000077161 BMID000000077162 BMID000000077163 BMID000000077164 BMID000000077165 BMID000000077166 BMID000000077167 BMID000000077168 BMID000000077169 BMID000000077170 BMID000000077171 BMID000000077172 BMID000000077173 BMID000000077174 BMID000000077175 BMID000000077176 BMID000000077177 BMID000000077178 BMID000000077179 BMID000000077180 BMID000000077181 BMID000000077182 BMID000000140791 BMID000000016540 BMID000000016541 BMID000000016542 BMID000000016543 BMID000000016544 BMID000000016545 BMID000000016546 BMID000000016547 BMID000000016548 BMID000000016549 BMID000000016550 BMID000000016551 BMID000000016552 BMID000000096115 BMID000000096116 BMID000000096117 BMID000000096118 BMID000000096119 BMID000000096120 BMID000000096121 BMID000000096122 BMID000000096123 BMID000000096124 BMID000000096125 BMID000000096126 BMID000000096127 BMID000000096128 BMID000000096129 BMID000000096130 BMID000000096131 BMID000000096132 BMID000000096133 BMID000000096134 BMID000000096135 BMID000000096136 BMID000000096137 BMID000000096138 BMID000000096139 BMID000000096140 BMID000000096141 BMID000000096142 BMID000000096143 BMID000000096144 BMID000000096145 BMID000000096146 BMID000000096147 BMID000000096148 BMID000000096149 BMID000000096150 BMID000000096151 BMID000000096152 BMID000000096153 .

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: BMID000000141817 | 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 - Orientia tsutsugamushi (strain Ikeda)

Publications

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

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