Dataset Information

Whole Genome Metabolism - Herbaspirillum seropedicae (strain SmR1)

ABSTRACT:

Whole Genome Metabolism of "Herbaspirillum seropedicae (strain SmR1)"

This is a whole genome metabolism model of Herbaspirillum seropedicae (strain SmR1).

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: BMID000000142011 .

Other models with the same genus include BMID000000001711 BMID000000001712 BMID000000001713 BMID000000001714 BMID000000001715 BMID000000001716 BMID000000001717 BMID000000001718 BMID000000001719 BMID000000001720 BMID000000001721 BMID000000001722 BMID000000001723 BMID000000001724 BMID000000001725 BMID000000001726 BMID000000001727 BMID000000035117 BMID000000035118 BMID000000035119 BMID000000035120 BMID000000035121 BMID000000035122 BMID000000035123 BMID000000035124 BMID000000035125 BMID000000035126 BMID000000035127 BMID000000035128 BMID000000035129 BMID000000035130 BMID000000035131 BMID000000035132 BMID000000035133 BMID000000035134 BMID000000035135 BMID000000035136 BMID000000035137 BMID000000035138 BMID000000035139 BMID000000035140 BMID000000035141 BMID000000035142 BMID000000035143 BMID000000035144 BMID000000035145 BMID000000035146 BMID000000035147 BMID000000035148 BMID000000035149 BMID000000035150 BMID000000035151 BMID000000035152 BMID000000035153 BMID000000035154 BMID000000035155 BMID000000035156 BMID000000035157 BMID000000035158 BMID000000035159 BMID000000035160 BMID000000035161 BMID000000035162 BMID000000035163 BMID000000035164 BMID000000035165 BMID000000035166 BMID000000035167 BMID000000035168 BMID000000035169 BMID000000035170 BMID000000035171 BMID000000035172 BMID000000035173 BMID000000035174 BMID000000035175 BMID000000035176 BMID000000035177 BMID000000035178 BMID000000035179 BMID000000035180 BMID000000035181 BMID000000035182 BMID000000035183 BMID000000035184 BMID000000035185 BMID000000035186 BMID000000035187 BMID000000035188 BMID000000035189 BMID000000035190 BMID000000035191 BMID000000035192 BMID000000035193 BMID000000035194 BMID000000035195 BMID000000035196 BMID000000035197 BMID000000035198 BMID000000035199 BMID000000035200 BMID000000035201 BMID000000035202 BMID000000035203 BMID000000035204 .

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: BMID000000142011 | 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 - Herbaspirillum seropedicae (strain SmR1)

Publications

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

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