Dataset Information

Whole Genome Metabolism - Symbiobacterium thermophilum (strain T / IAM 14863)

ABSTRACT:

Whole Genome Metabolism of "Symbiobacterium thermophilum IAM 14863"

This is a whole genome metabolism model of Symbiobacterium thermophilum IAM 14863.

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: BMID000000140918 .

Other models with the same genus include BMID000000003142 BMID000000003143 BMID000000003144 BMID000000003145 BMID000000003146 BMID000000003147 BMID000000003148 BMID000000003149 BMID000000003150 BMID000000003151 BMID000000003152 BMID000000003153 BMID000000003154 BMID000000003155 BMID000000003156 BMID000000003157 BMID000000003158 BMID000000040761 BMID000000040762 BMID000000040763 BMID000000040764 BMID000000040765 BMID000000040766 BMID000000040767 BMID000000040768 BMID000000040769 BMID000000040770 BMID000000040771 BMID000000040772 BMID000000040773 BMID000000040774 BMID000000040775 BMID000000040776 BMID000000040777 BMID000000040778 BMID000000040779 BMID000000040780 BMID000000040781 BMID000000040782 BMID000000040783 BMID000000040784 BMID000000040785 BMID000000040786 BMID000000040787 BMID000000040788 BMID000000040789 BMID000000040790 BMID000000040791 BMID000000040792 BMID000000040793 BMID000000040794 BMID000000040795 BMID000000040796 BMID000000040797 BMID000000040798 BMID000000040799 BMID000000040800 BMID000000040801 BMID000000040802 BMID000000040803 BMID000000040804 BMID000000040805 BMID000000040806 BMID000000040807 BMID000000040808 BMID000000040809 BMID000000040810 BMID000000040811 BMID000000040812 BMID000000040813 BMID000000040814 BMID000000040815 BMID000000040816 BMID000000040817 BMID000000040818 BMID000000040819 BMID000000040820 BMID000000040821 BMID000000040822 BMID000000040823 BMID000000040824 BMID000000040825 BMID000000040826 BMID000000040827 BMID000000040828 BMID000000040829 BMID000000040830 BMID000000040831 BMID000000040832 BMID000000040833 BMID000000040834 .

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: BMID000000140918 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

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Publications

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.

Ueda Kenji K Yamashita Atsushi A Ishikawa Jun J Shimada Masafumi M Watsuji Tomo-o TO Morimura Kohji K Ikeda Haruo H Hattori Masahira M Beppu Teruhiko T

Nucleic acids research 20040921 16

Symbiobacterium thermophilum is an uncultivable bacterium isolated from compost that depends on microbial commensalism. The 16S ribosomal DNA-based phylogeny suggests that this bacterium belongs to an unknown taxon in the Gram-positive bacterial cluster. Here, we describe the 3.57 Mb genome sequence of S.thermophilum. The genome consists of 3338 protein-coding sequences, out of which 2082 have functional assignments. Despite the high G + C content (68.7%), the genome is closest to that of Firmic ...[more]

PMID: 15383646

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 - Symbiobacterium thermophilum (strain T / IAM 14863)

Publications

Genome sequence of Symbiobacterium thermophilum, an uncultivable bacterium that depends on microbial commensalism.

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