Dataset Information

Whole Genome Metabolism - Psychrobacter cryohalolentis (strain K5)

ABSTRACT:

Whole Genome Metabolism of "Psychrobacter cryohalolentis (strain K5)"

This is a whole genome metabolism model of Psychrobacter cryohalolentis (strain K5).

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: BMID000000141879 .

Other models with the same genus include BMID000000005944 BMID000000005945 BMID000000005946 BMID000000005947 BMID000000005948 BMID000000005949 BMID000000005950 BMID000000005951 BMID000000005952 BMID000000005953 BMID000000005954 BMID000000005955 BMID000000005956 BMID000000051987 BMID000000051988 BMID000000051989 BMID000000051990 BMID000000051991 BMID000000051992 BMID000000051993 BMID000000051994 BMID000000051995 BMID000000051996 BMID000000051997 BMID000000051998 BMID000000051999 BMID000000052000 BMID000000052001 BMID000000052002 BMID000000052003 BMID000000052004 BMID000000052005 BMID000000052006 BMID000000052007 BMID000000052008 BMID000000052009 BMID000000052010 BMID000000052011 BMID000000052012 BMID000000052013 BMID000000052014 BMID000000052015 BMID000000052016 BMID000000052017 BMID000000052018 BMID000000052019 BMID000000052020 BMID000000052021 BMID000000052022 BMID000000052023 BMID000000052024 BMID000000052025 BMID000000052026 BMID000000052027 BMID000000052028 BMID000000052029 BMID000000052030 BMID000000052031 BMID000000052032 BMID000000052033 BMID000000052034 BMID000000052035 BMID000000052036 BMID000000052037 BMID000000052038 BMID000000052039 BMID000000052040 BMID000000052041 BMID000000052042 BMID000000052043 BMID000000052044 BMID000000052045 BMID000000052046 BMID000000052047 BMID000000052048 BMID000000052049 BMID000000052050 BMID000000052051 BMID000000052052 BMID000000052053 BMID000000052054 BMID000000052055 BMID000000052056 BMID000000052057 BMID000000052058 BMID000000052059 BMID000000052060 BMID000000052061 BMID000000052062 BMID000000052063 BMID000000141787 BMID000000008319 BMID000000008320 BMID000000008321 BMID000000008322 BMID000000008323 BMID000000008324 BMID000000008325 BMID000000008326 BMID000000008327 BMID000000008328 BMID000000008329 BMID000000008330 BMID000000008331 BMID000000063087 BMID000000063088 BMID000000063089 BMID000000063090 BMID000000063091 BMID000000063092 BMID000000063093 BMID000000063094 BMID000000063095 BMID000000063096 BMID000000063097 BMID000000063098 BMID000000063099 BMID000000063100 BMID000000063101 BMID000000063102 BMID000000063103 BMID000000063104 BMID000000063105 BMID000000063106 BMID000000063107 BMID000000063108 BMID000000063109 BMID000000063110 BMID000000063111 BMID000000063112 BMID000000063113 BMID000000063114 BMID000000063115 BMID000000063116 BMID000000063117 BMID000000063118 BMID000000063119 BMID000000063120 BMID000000063121 BMID000000063122 BMID000000063123 BMID000000063124 BMID000000063125 BMID000000063126 BMID000000063127 BMID000000063128 BMID000000063129 BMID000000063130 BMID000000063131 BMID000000063132 BMID000000063133 BMID000000063134 BMID000000063135 BMID000000063136 BMID000000063137 BMID000000063138 BMID000000063139 BMID000000063140 BMID000000063141 BMID000000063142 BMID000000063143 BMID000000063144 BMID000000063145 BMID000000063146 BMID000000063147 BMID000000063148 BMID000000063149 BMID000000063150 BMID000000063151 BMID000000063152 BMID000000063153 BMID000000063154 BMID000000063155 BMID000000063156 BMID000000063157 BMID000000063158 BMID000000063159 BMID000000063160 BMID000000063161 BMID000000063162 BMID000000063163 BMID000000063164 BMID000000063165 BMID000000063166 BMID000000063167 BMID000000063168 BMID000000063169 BMID000000141707 BMID000000016334 BMID000000016335 BMID000000016336 BMID000000016337 BMID000000016338 BMID000000016339 BMID000000016340 BMID000000016341 BMID000000016342 BMID000000016343 BMID000000016344 BMID000000016345 BMID000000016346 BMID000000016347 BMID000000095695 BMID000000095696 BMID000000095697 BMID000000095698 BMID000000095699 BMID000000095700 BMID000000095701 BMID000000095702 BMID000000095703 BMID000000095704 BMID000000095705 BMID000000095706 BMID000000095707 BMID000000095708 BMID000000095709 BMID000000095710 BMID000000095711 BMID000000095712 BMID000000095713 BMID000000095714 BMID000000095715 BMID000000095716 BMID000000095717 BMID000000095718 BMID000000095719 BMID000000095720 BMID000000095721 BMID000000095722 BMID000000095723 BMID000000095724 BMID000000095725 BMID000000095726 BMID000000095727 BMID000000095728 BMID000000095729 BMID000000095730 BMID000000095731 BMID000000095732 BMID000000095733 BMID000000095734 BMID000000095735 BMID000000095736 BMID000000095737 BMID000000095738 BMID000000095739 BMID000000095740 BMID000000095741 BMID000000095742 BMID000000095743 BMID000000095744 BMID000000095745 BMID000000095746 BMID000000095747 BMID000000095748 BMID000000095749 BMID000000095750 BMID000000095751 BMID000000095752 BMID000000095753 BMID000000095754 BMID000000095755 BMID000000095756 BMID000000095757 BMID000000095758 BMID000000095759 BMID000000095760 BMID000000095761 BMID000000095762 BMID000000095763 BMID000000095764 BMID000000095765 BMID000000095766 BMID000000095767 BMID000000095768 BMID000000095769 BMID000000095770 BMID000000095771 BMID000000095772 BMID000000095773 BMID000000095774 BMID000000095775 BMID000000095776 BMID000000095777 BMID000000095778 BMID000000095779 .

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: BMID000000141879 | 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 - Psychrobacter cryohalolentis (strain K5)

Publications

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

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