Dataset Information

Whole Genome Metabolism - Bartonella tribocorum (strain CIP 105476 / IBS 506)

ABSTRACT:

Whole Genome Metabolism of "Bartonella tribocorum (strain CIP 105476 / IBS 506)"

This is a whole genome metabolism model of Bartonella tribocorum (strain CIP 105476 / IBS 506).

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: BMID000000140298 .

Other models with the same genus include BMID000000001019 BMID000000001020 BMID000000001021 BMID000000001022 BMID000000001023 BMID000000001024 BMID000000001025 BMID000000001026 BMID000000001027 BMID000000001028 BMID000000001029 BMID000000001030 BMID000000001031 BMID000000001032 BMID000000031863 BMID000000031864 BMID000000031865 BMID000000031866 BMID000000031867 BMID000000031868 BMID000000031869 BMID000000031870 BMID000000031871 BMID000000031872 BMID000000031873 BMID000000031874 BMID000000031875 BMID000000031876 BMID000000031877 BMID000000031878 BMID000000031879 BMID000000031880 BMID000000031881 BMID000000031882 BMID000000031883 BMID000000031884 BMID000000031885 BMID000000031886 BMID000000031887 BMID000000031888 BMID000000031889 BMID000000031890 BMID000000031891 BMID000000031892 BMID000000031893 BMID000000031894 BMID000000031895 BMID000000031896 BMID000000031897 BMID000000031898 BMID000000031899 BMID000000031900 BMID000000031901 BMID000000031902 BMID000000031903 BMID000000031904 BMID000000031905 BMID000000031906 BMID000000031907 BMID000000031908 BMID000000031909 BMID000000031910 BMID000000031911 BMID000000031912 BMID000000031913 BMID000000031914 BMID000000031915 BMID000000031916 BMID000000031917 BMID000000031918 BMID000000031919 BMID000000031920 BMID000000031921 BMID000000031922 BMID000000031923 BMID000000031924 BMID000000031925 BMID000000031926 BMID000000031927 BMID000000031928 BMID000000031929 BMID000000031930 BMID000000031931 BMID000000031932 BMID000000031933 BMID000000006328 BMID000000006329 BMID000000006330 BMID000000006331 BMID000000006332 BMID000000006333 BMID000000006334 BMID000000006335 BMID000000006336 BMID000000006337 BMID000000006338 BMID000000006339 BMID000000006340 BMID000000006341 BMID000000053825 BMID000000053826 BMID000000053827 BMID000000053828 BMID000000053829 BMID000000053830 BMID000000053831 BMID000000053832 BMID000000053833 BMID000000053834 BMID000000053835 BMID000000053836 BMID000000053837 BMID000000053838 BMID000000053839 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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: BMID000000140298 | 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 - Bartonella tribocorum (strain CIP 105476 / IBS 506)

Publications

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

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