Dataset Information

Whole Genome Metabolism - Onion yellows phytoplasma (strain OY-M)

ABSTRACT:

Whole Genome Metabolism of "Onion yellows phytoplasma (strain OY-M)"

This is a whole genome metabolism model of Onion yellows phytoplasma (strain OY-M).

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: BMID000000141711 .

Other models with the same genus include BMID000000000719 BMID000000000720 BMID000000000721 BMID000000000722 BMID000000000723 BMID000000000724 BMID000000000725 BMID000000000726 BMID000000000727 BMID000000000728 BMID000000000729 BMID000000000730 BMID000000000731 BMID000000030424 BMID000000030425 BMID000000030426 BMID000000030427 BMID000000030428 BMID000000030429 BMID000000030430 BMID000000030431 BMID000000030432 BMID000000030433 BMID000000030434 BMID000000030435 BMID000000030436 BMID000000030437 BMID000000030438 BMID000000030439 BMID000000030440 BMID000000030441 BMID000000030442 BMID000000030443 BMID000000030444 BMID000000030445 BMID000000030446 BMID000000030447 .

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: BMID000000141711 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

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Publications

Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma.

Oshima Kenro K Kakizawa Shigeyuki S Nishigawa Hisashi H Jung Hee-Young HY Wei Wei W Suzuki Shiho S Arashida Ryo R Nakata Daisuke D Miyata Shin-ichi S Ugaki Masashi M Namba Shigetou S

Nature genetics 20031207 1

The minimal gene set essential for life has long been sought. We report the 860-kb genome of the obligate intracellular plant pathogen phytoplasma (Candidatus Phytoplasma asteris, OY strain). The phytoplasma genome encodes even fewer metabolic functions than do mycoplasma genomes. It lacks the pentose phosphate cycle and, more unexpectedly, ATP-synthase subunits, which are thought to be essential for life. This may be the result of reductive evolution as a consequence of life as an intracellular ...[more]

PMID: 14661021

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 - Onion yellows phytoplasma (strain OY-M)

Publications

Reductive evolution suggested from the complete genome sequence of a plant-pathogenic phytoplasma.

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