Dataset Information

Whole Genome Metabolism - Elusimicrobium minutum (strain Pei191)

ABSTRACT:

Whole Genome Metabolism of "Elusimicrobium minutum (strain Pei191)"

This is a whole genome metabolism model of Elusimicrobium minutum (strain Pei191).

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: BMID000000140931 .

Other models with the same genus include BMID000000005168 BMID000000005169 BMID000000005170 BMID000000005171 BMID000000005172 BMID000000005173 BMID000000005174 BMID000000005175 BMID000000005176 BMID000000005177 BMID000000005178 BMID000000005179 BMID000000005180 BMID000000005181 BMID000000048522 BMID000000048523 BMID000000048524 BMID000000048525 BMID000000048526 BMID000000048527 BMID000000048528 BMID000000048529 BMID000000048530 BMID000000048531 BMID000000048532 BMID000000048533 BMID000000048534 BMID000000048535 BMID000000048536 BMID000000048537 BMID000000048538 BMID000000048539 BMID000000048540 BMID000000048541 BMID000000048542 BMID000000048543 BMID000000048544 BMID000000048545 BMID000000048546 BMID000000048547 BMID000000048548 BMID000000048549 BMID000000048550 BMID000000048551 BMID000000048552 BMID000000048553 BMID000000048554 BMID000000048555 BMID000000048556 BMID000000048557 BMID000000048558 BMID000000048559 BMID000000048560 BMID000000048561 BMID000000048562 BMID000000048563 BMID000000048564 BMID000000048565 BMID000000048566 BMID000000048567 BMID000000048568 BMID000000048569 BMID000000048570 BMID000000048571 BMID000000048572 BMID000000048573 BMID000000048574 BMID000000048575 BMID000000048576 BMID000000048577 BMID000000048578 BMID000000048579 BMID000000048580 BMID000000048581 BMID000000048582 .

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: BMID000000140931 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

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Publications

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1).

Herlemann D P R DP Geissinger O O Ikeda-Ohtsubo W W Kunin V V Sun H H Lapidus A A Hugenholtz P P Brune A A

Applied and environmental microbiology 20090306 9

Organisms of the candidate phylum termite group 1 (TG1) are regularly encountered in termite hindguts but are present also in many other habitats. Here, we report the complete genome sequence (1.64 Mbp) of "Elusimicrobium minutum" strain Pei191(T), the first cultured representative of the TG1 phylum. We reconstructed the metabolism of this strictly anaerobic bacterium isolated from a beetle larva gut, and we discuss the findings in light of physiological data. E. minutum has all genes required f ...[more]

PMID: 19270133

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 - Elusimicrobium minutum (strain Pei191)

Publications

Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1).

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