Dataset Information

Whole Genome Metabolism - Phytophthora infestans (strain T30-4)

ABSTRACT:

Whole Genome Metabolism of "Phytophthora infestans (strain T30-4)"

This is a whole genome metabolism model of Phytophthora infestans (strain T30-4).

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: BMID000000140564 .

Other models with the same genus include BMID000000010167 BMID000000010168 BMID000000010169 BMID000000010170 BMID000000010171 BMID000000010172 BMID000000010173 BMID000000010174 BMID000000010175 BMID000000010176 BMID000000010177 BMID000000010178 BMID000000010179 BMID000000010180 BMID000000010181 BMID000000010182 BMID000000010183 BMID000000010184 BMID000000010185 BMID000000010186 BMID000000010187 BMID000000010188 BMID000000010189 BMID000000010190 BMID000000010191 BMID000000010192 BMID000000010193 BMID000000069998 BMID000000069999 BMID000000070000 BMID000000070001 BMID000000070002 BMID000000070003 BMID000000070004 BMID000000070005 BMID000000070006 BMID000000070007 BMID000000070008 BMID000000070009 BMID000000070010 BMID000000070011 BMID000000070012 BMID000000070013 BMID000000070014 BMID000000070015 BMID000000070016 BMID000000070017 BMID000000070018 BMID000000070019 BMID000000070020 BMID000000070021 BMID000000070022 BMID000000070023 BMID000000070024 BMID000000070025 BMID000000070026 BMID000000070027 BMID000000070028 BMID000000070029 BMID000000070030 BMID000000070031 BMID000000070032 BMID000000070033 BMID000000070034 BMID000000070035 BMID000000070036 BMID000000070037 BMID000000070038 BMID000000070039 BMID000000070040 BMID000000070041 BMID000000070042 BMID000000070043 BMID000000070044 BMID000000070045 BMID000000070046 BMID000000070047 BMID000000070048 BMID000000070049 BMID000000070050 BMID000000070051 BMID000000070052 BMID000000070053 BMID000000070054 BMID000000070055 BMID000000070056 BMID000000070057 BMID000000070058 BMID000000070059 BMID000000070060 BMID000000070061 BMID000000070062 BMID000000070063 BMID000000070064 BMID000000070065 BMID000000070066 .

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: BMID000000140564 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

Haas Brian J BJ Kamoun Sophien S Zody Michael C MC Jiang Rays H Y RH Handsaker Robert E RE Cano Liliana M LM Grabherr Manfred M Kodira Chinnappa D CD Raffaele Sylvain S Torto-Alalibo Trudy T Bozkurt Tolga O TO Ah-Fong Audrey M V AM Alvarado Lucia L Anderson Vicky L VL Armstrong Miles R MR Avrova Anna A Baxter Laura L Beynon Jim J Boevink Petra C PC Bollmann Stephanie R SR Bos Jorunn I B JI Bulone Vincent V Cai Guohong G Cakir Cahid C Carrington James C JC Chawner Megan M Conti Lucio L Costanzo Stefano S Ewan Richard R Fahlgren Noah N Fischbach Michael A MA Fugelstad Johanna J Gilroy Eleanor M EM Gnerre Sante S Green Pamela J PJ Grenville-Briggs Laura J LJ Griffith John J Grünwald Niklaus J NJ Horn Karolyn K Horner Neil R NR Hu Chia-Hui CH Huitema Edgar E Jeong Dong-Hoon DH Jones Alexandra M E AM Jones Jonathan D G JD Jones Richard W RW Karlsson Elinor K EK Kunjeti Sridhara G SG Lamour Kurt K Liu Zhenyu Z Ma Lijun L Maclean Daniel D Chibucos Marcus C MC McDonald Hayes H McWalters Jessica J Meijer Harold J G HJ Morgan William W Morris Paul F PF Munro Carol A CA O'Neill Keith K Ospina-Giraldo Manuel M Pinzón Andrés A Pritchard Leighton L Ramsahoye Bernard B Ren Qinghu Q Restrepo Silvia S Roy Sourav S Sadanandom Ari A Savidor Alon A Schornack Sebastian S Schwartz David C DC Schumann Ulrike D UD Schwessinger Ben B Seyer Lauren L Sharpe Ted T Silvar Cristina C Song Jing J Studholme David J DJ Sykes Sean S Thines Marco M van de Vondervoort Peter J I PJ Phuntumart Vipaporn V Wawra Stephan S Weide Rob R Win Joe J Young Carolyn C Zhou Shiguo S Fry William W Meyers Blake C BC van West Pieter P Ristaino Jean J Govers Francine F Birch Paul R J PR Whisson Stephen C SC Judelson Howard S HS Nusbaum Chad C

Nature 20090909 7262

Phytophthora infestans is the most destructive pathogen of potato and a model organism for the oomycetes, a distinct lineage of fungus-like eukaryotes that are related to organisms such as brown algae and diatoms. As the agent of the Irish potato famine in the mid-nineteenth century, P. infestans has had a tremendous effect on human history, resulting in famine and population displacement. To this day, it affects world agriculture by causing the most destructive disease of potato, the fourth lar ...[more]

PMID: 19741609

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 - Phytophthora infestans (strain T30-4)

Publications

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.

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