Dataset Information

Whole Genome Metabolism - Macrococcus caseolyticus (strain JCSC5402)

ABSTRACT:

Whole Genome Metabolism of "Macrococcus caseolyticus (strain JCSC5402)"

This is a whole genome metabolism model of Macrococcus caseolyticus (strain JCSC5402).

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: BMID000000140841 .

Other models with the same genus include BMID000000005930 BMID000000005931 BMID000000005932 BMID000000005933 BMID000000005934 BMID000000005935 BMID000000005936 BMID000000005937 BMID000000005938 BMID000000005939 BMID000000005940 BMID000000005941 BMID000000005942 BMID000000005943 BMID000000051918 BMID000000051919 BMID000000051920 BMID000000051921 BMID000000051922 BMID000000051923 BMID000000051924 BMID000000051925 BMID000000051926 BMID000000051927 BMID000000051928 BMID000000051929 BMID000000051930 BMID000000051931 BMID000000051932 BMID000000051933 BMID000000051934 BMID000000051935 BMID000000051936 BMID000000051937 BMID000000051938 BMID000000051939 BMID000000051940 BMID000000051941 BMID000000051942 BMID000000051943 BMID000000051944 BMID000000051945 BMID000000051946 BMID000000051947 BMID000000051948 BMID000000051949 BMID000000051950 BMID000000051951 BMID000000051952 BMID000000051953 BMID000000051954 BMID000000051955 BMID000000051956 BMID000000051957 BMID000000051958 BMID000000051959 BMID000000051960 BMID000000051961 BMID000000051962 BMID000000051963 BMID000000051964 BMID000000051965 BMID000000051966 BMID000000051967 BMID000000051968 BMID000000051969 BMID000000051970 BMID000000051971 BMID000000051972 BMID000000051973 BMID000000051974 BMID000000051975 BMID000000051976 BMID000000051977 BMID000000051978 BMID000000051979 BMID000000051980 BMID000000051981 BMID000000051982 BMID000000051983 BMID000000051984 BMID000000051985 BMID000000051986 .

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: BMID000000140841 | 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 - Macrococcus caseolyticus (strain JCSC5402)

Publications

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

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