Dataset Information

Whole Genome Metabolism - Pyrobaculum calidifontis (strain JCM 11548 / VA1)

ABSTRACT:

Whole Genome Metabolism of "Pyrobaculum calidifontis (strain JCM 11548 / VA1)"

This is a whole genome metabolism model of Pyrobaculum calidifontis (strain JCM 11548 / VA1).

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: BMID000000140479 .

Other models with the same genus include BMID000000003222 BMID000000003223 BMID000000003224 BMID000000003225 BMID000000003226 BMID000000003227 BMID000000003228 BMID000000003229 BMID000000003230 BMID000000003231 BMID000000003232 BMID000000003233 BMID000000003234 BMID000000003235 BMID000000003236 BMID000000041110 BMID000000041111 BMID000000041112 BMID000000041113 BMID000000041114 BMID000000041115 BMID000000041116 BMID000000041117 BMID000000041118 BMID000000041119 BMID000000041120 BMID000000041121 BMID000000041122 BMID000000041123 BMID000000041124 BMID000000041125 BMID000000041126 BMID000000041127 BMID000000041128 BMID000000041129 BMID000000041130 BMID000000041131 BMID000000041132 BMID000000041133 BMID000000041134 BMID000000041135 BMID000000041136 BMID000000041137 BMID000000041138 BMID000000041139 BMID000000041140 BMID000000041141 BMID000000041142 BMID000000041143 BMID000000041144 BMID000000041145 BMID000000041146 BMID000000041147 BMID000000041148 BMID000000041149 BMID000000041150 BMID000000041151 BMID000000041152 BMID000000041153 BMID000000041154 BMID000000041155 BMID000000041156 BMID000000041157 BMID000000041158 BMID000000041159 BMID000000041160 BMID000000041161 BMID000000041162 BMID000000041163 BMID000000041164 BMID000000041165 BMID000000041166 BMID000000041167 BMID000000041168 BMID000000041169 BMID000000041170 BMID000000041171 BMID000000041172 BMID000000041173 BMID000000041174 BMID000000141600 BMID000000007996 BMID000000007997 BMID000000007998 BMID000000007999 BMID000000008000 BMID000000008001 BMID000000008002 BMID000000008003 BMID000000008004 BMID000000008005 BMID000000008006 BMID000000008007 BMID000000008008 BMID000000008009 BMID000000008010 BMID000000061737 BMID000000061738 BMID000000061739 BMID000000061740 BMID000000061741 BMID000000061742 BMID000000061743 BMID000000061744 BMID000000061745 BMID000000061746 BMID000000061747 BMID000000061748 BMID000000061749 BMID000000061750 BMID000000061751 BMID000000061752 BMID000000061753 BMID000000061754 BMID000000061755 BMID000000061756 BMID000000061757 BMID000000061758 BMID000000061759 BMID000000061760 BMID000000061761 BMID000000061762 BMID000000061763 BMID000000061764 BMID000000061765 BMID000000061766 BMID000000061767 BMID000000061768 BMID000000061769 BMID000000061770 BMID000000061771 BMID000000061772 BMID000000061773 BMID000000061774 BMID000000061775 BMID000000061776 BMID000000061777 BMID000000061778 BMID000000061779 BMID000000061780 BMID000000061781 BMID000000061782 BMID000000061783 BMID000000061784 BMID000000061785 BMID000000061786 BMID000000061787 BMID000000061788 BMID000000061789 BMID000000061790 BMID000000061791 BMID000000061792 BMID000000061793 BMID000000061794 BMID000000061795 BMID000000061796 BMID000000061797 BMID000000061798 BMID000000061799 BMID000000061800 BMID000000061801 BMID000000061802 BMID000000061803 BMID000000021860 BMID000000021861 BMID000000021862 BMID000000021863 BMID000000021864 BMID000000021865 BMID000000021866 BMID000000021867 BMID000000021868 BMID000000021869 BMID000000021870 BMID000000021871 BMID000000021872 BMID000000021873 BMID000000021874 BMID000000117920 BMID000000117921 BMID000000117922 BMID000000117923 BMID000000117924 BMID000000117925 BMID000000117926 BMID000000117927 BMID000000117928 BMID000000117929 BMID000000117930 BMID000000117931 BMID000000117932 BMID000000117933 BMID000000117934 BMID000000117935 BMID000000117936 BMID000000117937 BMID000000117938 BMID000000117939 BMID000000117940 BMID000000117941 BMID000000117942 BMID000000117943 BMID000000117944 BMID000000117945 BMID000000117946 BMID000000117947 BMID000000117948 BMID000000117949 BMID000000117950 BMID000000117951 BMID000000117952 BMID000000117953 BMID000000117954 BMID000000117955 BMID000000117956 BMID000000117957 BMID000000117958 BMID000000117959 BMID000000117960 BMID000000117961 BMID000000117962 BMID000000117963 BMID000000117964 BMID000000117965 BMID000000117966 BMID000000117967 BMID000000117968 BMID000000117969 BMID000000117970 BMID000000117971 BMID000000117972 BMID000000117973 BMID000000117974 BMID000000117975 BMID000000117976 BMID000000117977 BMID000000117978 BMID000000117979 BMID000000117980 BMID000000117981 BMID000000117982 BMID000000117983 BMID000000141112 BMID000000022842 BMID000000022843 BMID000000022844 BMID000000022845 BMID000000022846 BMID000000022847 BMID000000022848 BMID000000022849 BMID000000022850 BMID000000022851 BMID000000022852 BMID000000022853 BMID000000022854 BMID000000022855 BMID000000022856 BMID000000122126 BMID000000122127 BMID000000122128 BMID000000122129 BMID000000122130 BMID000000122131 BMID000000122132 BMID000000122133 BMID000000122134 BMID000000122135 BMID000000122136 BMID000000122137 BMID000000122138 BMID000000122139 BMID000000122140 BMID000000122141 BMID000000122142 BMID000000122143 BMID000000122144 BMID000000122145 BMID000000122146 BMID000000122147 BMID000000122148 BMID000000122149 BMID000000122150 BMID000000122151 BMID000000122152 BMID000000122153 BMID000000122154 BMID000000122155 BMID000000122156 BMID000000122157 BMID000000122158 BMID000000122159 BMID000000122160 BMID000000122161 BMID000000122162 BMID000000122163 BMID000000122164 BMID000000122165 BMID000000122166 BMID000000122167 BMID000000122168 BMID000000122169 BMID000000122170 BMID000000122171 BMID000000122172 BMID000000122173 BMID000000122174 BMID000000122175 BMID000000122176 BMID000000122177 BMID000000122178 BMID000000122179 BMID000000122180 BMID000000122181 BMID000000122182 BMID000000122183 BMID000000122184 BMID000000122185 BMID000000122186 BMID000000122187 BMID000000122188 BMID000000122189 BMID000000122190 BMID000000122191 BMID000000122192 BMID000000141621 BMID000000141866 BMID000000142021 .

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: BMID000000140479 | 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 - Pyrobaculum calidifontis (strain JCM 11548 / VA1)

Publications

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

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