Dataset Information

Whole Genome Metabolism - Frankia alni (strain ACN14a)

ABSTRACT:

Whole Genome Metabolism of "Frankia alni (strain ACN14a)"

This is a whole genome metabolism model of Frankia alni (strain ACN14a).

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: BMID000000141887 .

Other models with the same genus include BMID000000004328 BMID000000004329 BMID000000004330 BMID000000004331 BMID000000004332 BMID000000004333 BMID000000004334 BMID000000004335 BMID000000004336 BMID000000004337 BMID000000004338 BMID000000004339 BMID000000004340 BMID000000004341 BMID000000045799 BMID000000045800 BMID000000045801 BMID000000045802 BMID000000045803 BMID000000045804 BMID000000045805 BMID000000045806 BMID000000045807 BMID000000045808 BMID000000045809 BMID000000045810 BMID000000045811 BMID000000045812 BMID000000045813 BMID000000045814 BMID000000045815 BMID000000045816 BMID000000045817 BMID000000045818 BMID000000045819 BMID000000045820 BMID000000045821 BMID000000045822 BMID000000045823 BMID000000045824 BMID000000045825 BMID000000045826 BMID000000045827 BMID000000045828 BMID000000045829 BMID000000045830 BMID000000045831 BMID000000045832 BMID000000045833 BMID000000045834 BMID000000045835 BMID000000045836 BMID000000045837 BMID000000045838 BMID000000045839 BMID000000045840 BMID000000045841 BMID000000045842 BMID000000045843 BMID000000045844 BMID000000045845 BMID000000045846 BMID000000045847 BMID000000045848 BMID000000045849 BMID000000045850 BMID000000045851 BMID000000045852 BMID000000045853 BMID000000045854 BMID000000045855 BMID000000045856 BMID000000045857 BMID000000045858 BMID000000045859 BMID000000045860 BMID000000045861 BMID000000045862 BMID000000045863 BMID000000045864 BMID000000045865 BMID000000045866 BMID000000045867 BMID000000045868 BMID000000045869 BMID000000045870 BMID000000045871 BMID000000045872 BMID000000045873 BMID000000045874 BMID000000045875 BMID000000045876 BMID000000045877 BMID000000045878 BMID000000045879 BMID000000045880 BMID000000045881 BMID000000045882 BMID000000045883 BMID000000045884 BMID000000045885 BMID000000045886 BMID000000141196 BMID000000006878 BMID000000006879 BMID000000006880 BMID000000006881 BMID000000006882 BMID000000006883 BMID000000006884 BMID000000006885 BMID000000006886 BMID000000006887 BMID000000006888 BMID000000006889 BMID000000006890 BMID000000006891 BMID000000006892 BMID000000056569 BMID000000056570 BMID000000056571 BMID000000056572 BMID000000056573 BMID000000056574 BMID000000056575 BMID000000056576 BMID000000056577 BMID000000056578 BMID000000056579 BMID000000056580 BMID000000056581 BMID000000056582 BMID000000056583 BMID000000056584 BMID000000056585 BMID000000056586 BMID000000056587 BMID000000056588 BMID000000056589 BMID000000056590 BMID000000056591 BMID000000056592 BMID000000056593 BMID000000056594 BMID000000056595 BMID000000056596 BMID000000056597 BMID000000056598 BMID000000056599 BMID000000056600 BMID000000056601 BMID000000056602 BMID000000056603 BMID000000056604 BMID000000056605 BMID000000056606 BMID000000056607 BMID000000056608 BMID000000056609 BMID000000056610 BMID000000056611 BMID000000056612 BMID000000056613 BMID000000056614 BMID000000056615 BMID000000056616 BMID000000056617 BMID000000056618 BMID000000056619 BMID000000056620 BMID000000056621 BMID000000056622 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BMID000000064197 BMID000000064198 BMID000000064199 BMID000000064200 BMID000000064201 BMID000000064202 BMID000000064203 BMID000000064204 BMID000000064205 BMID000000064206 BMID000000064207 BMID000000064208 BMID000000064209 BMID000000064210 BMID000000064211 BMID000000064212 BMID000000064213 BMID000000064214 BMID000000064215 BMID000000064216 BMID000000064217 BMID000000064218 BMID000000064219 BMID000000064220 BMID000000064221 BMID000000064222 BMID000000064223 BMID000000064224 BMID000000064225 BMID000000064226 BMID000000064227 BMID000000064228 BMID000000064229 BMID000000064230 BMID000000064231 BMID000000064232 BMID000000064233 BMID000000064234 BMID000000064235 BMID000000064236 BMID000000064237 BMID000000064238 BMID000000064239 BMID000000064240 BMID000000064241 BMID000000064242 BMID000000064243 BMID000000064244 BMID000000064245 BMID000000064246 BMID000000064247 BMID000000064248 BMID000000064249 BMID000000064250 BMID000000064251 BMID000000064252 BMID000000064253 BMID000000064254 BMID000000064255 BMID000000064256 BMID000000064257 BMID000000064258 BMID000000064259 BMID000000064260 BMID000000064261 BMID000000064262 BMID000000064263 BMID000000064264 BMID000000064265 BMID000000064266 BMID000000064267 BMID000000064268 BMID000000064269 BMID000000064270 BMID000000064271 BMID000000064272 BMID000000064273 BMID000000064274 BMID000000064275 BMID000000064276 BMID000000064277 BMID000000064278 BMID000000064279 BMID000000064280 BMID000000064281 BMID000000064282 BMID000000064283 BMID000000064284 BMID000000064285 BMID000000064286 BMID000000140588 BMID000000015323 BMID000000015324 BMID000000015325 BMID000000015326 BMID000000015327 BMID000000015328 BMID000000015329 BMID000000015330 BMID000000015331 BMID000000015332 BMID000000015333 BMID000000015334 BMID000000015335 BMID000000015336 BMID000000015337 BMID000000091765 BMID000000091766 BMID000000091767 BMID000000091768 BMID000000091769 BMID000000091770 BMID000000091771 BMID000000091772 BMID000000091773 BMID000000091774 BMID000000091775 BMID000000091776 BMID000000091777 BMID000000091778 BMID000000091779 BMID000000091780 BMID000000091781 BMID000000091782 BMID000000091783 BMID000000091784 BMID000000091785 BMID000000091786 BMID000000091787 BMID000000091788 BMID000000091789 BMID000000091790 BMID000000091791 BMID000000091792 BMID000000091793 BMID000000091794 BMID000000091795 BMID000000091796 BMID000000091797 BMID000000091798 BMID000000091799 BMID000000091800 BMID000000091801 BMID000000091802 BMID000000091803 BMID000000091804 BMID000000091805 BMID000000091806 BMID000000091807 BMID000000091808 BMID000000091809 BMID000000091810 BMID000000091811 BMID000000091812 BMID000000091813 BMID000000091814 BMID000000091815 BMID000000091816 BMID000000091817 BMID000000091818 BMID000000091819 BMID000000091820 BMID000000091821 BMID000000091822 BMID000000091823 BMID000000091824 BMID000000091825 BMID000000091826 BMID000000091827 BMID000000091828 BMID000000091829 BMID000000091830 BMID000000091831 BMID000000091832 BMID000000091833 BMID000000091834 BMID000000091835 BMID000000091836 BMID000000091837 BMID000000091838 BMID000000091839 BMID000000091840 BMID000000091841 BMID000000091842 BMID000000091843 BMID000000091844 BMID000000091845 BMID000000091846 BMID000000091847 BMID000000091848 BMID000000091849 BMID000000091850 BMID000000091851 BMID000000091852 BMID000000091853 BMID000000091854 BMID000000141038 .

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: BMID000000141887 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

Normand Philippe P Lapierre Pascal P Tisa Louis S LS Gogarten Johann Peter JP Alloisio Nicole N Bagnarol Emilie E Bassi Carla A CA Berry Alison M AM Bickhart Derek M DM Choisne Nathalie N Couloux Arnaud A Cournoyer Benoit B Cruveiller Stephane S Daubin Vincent V Demange Nadia N Francino Maria Pilar MP Goltsman Eugene E Huang Ying Y Kopp Olga R OR Labarre Laurent L Lapidus Alla A Lavire Celine C Marechal Joelle J Martinez Michele M Mastronunzio Juliana E JE Mullin Beth C BC Niemann James J Pujic Pierre P Rawnsley Tania T Rouy Zoe Z Schenowitz Chantal C Sellstedt Anita A Tavares Fernando F Tomkins Jeffrey P JP Vallenet David D Valverde Claudio C Wall Luis G LG Wang Ying Y Medigue Claudine C Benson David R DR

Genome research 20061206 1

Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade ...[more]

PMID: 17151343

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 - Frankia alni (strain ACN14a)

Publications

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.

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