Dataset Information

Whole Genome Metabolism - Dichelobacter nodosus (strain VCS1703A)

ABSTRACT:

Whole Genome Metabolism of "Dichelobacter nodosus (strain VCS1703A)"

This is a whole genome metabolism model of Dichelobacter nodosus (strain VCS1703A).

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: BMID000000140863 .

Other models with the same genus include BMID000000027292 BMID000000027293 BMID000000027294 BMID000000027295 BMID000000027296 BMID000000027297 BMID000000027298 BMID000000027299 BMID000000027300 BMID000000027301 BMID000000027302 BMID000000027303 BMID000000027304 BMID000000027305 BMID000000027306 BMID000000140148 BMID000000140149 BMID000000140150 BMID000000140151 BMID000000140152 BMID000000140153 BMID000000140154 BMID000000140155 BMID000000140156 BMID000000140157 BMID000000140158 BMID000000140159 BMID000000140160 BMID000000140161 BMID000000140162 BMID000000140163 BMID000000140164 BMID000000140165 BMID000000140166 BMID000000140167 BMID000000140168 BMID000000140169 BMID000000140170 BMID000000140171 BMID000000140172 BMID000000140173 BMID000000140174 BMID000000140175 BMID000000140176 BMID000000140177 BMID000000140178 BMID000000140179 BMID000000140180 BMID000000140181 BMID000000140182 BMID000000140183 BMID000000140184 BMID000000140185 BMID000000140186 BMID000000140187 BMID000000140188 BMID000000140189 BMID000000140190 BMID000000140191 BMID000000140192 BMID000000140193 BMID000000140194 BMID000000140195 BMID000000140196 BMID000000140197 BMID000000140198 BMID000000140199 BMID000000140200 BMID000000140201 BMID000000140202 BMID000000140203 BMID000000140204 .

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: BMID000000140863 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

Myers Garry S A GS Parker Dane D Al-Hasani Keith K Kennan Ruth M RM Seemann Torsten T Ren Qinghu Q Badger Jonathan H JH Selengut Jeremy D JD Deboy Robert T RT Tettelin Hervé H Boyce John D JD McCarl Victoria P VP Han Xiaoyan X Nelson William C WC Madupu Ramana R Mohamoud Yasmin Y Holley Tara T Fedorova Nadia N Khouri Hoda H Bottomley Steven P SP Whittington Richard J RJ Adler Ben B Songer J Glenn JG Rood Julian I JI Paulsen Ian T IT

Nature biotechnology 20070429 5

Dichelobacter nodosus causes ovine footrot, a disease that leads to severe economic losses in the wool and meat industries. We sequenced its 1.4-Mb genome, the smallest known genome of an anaerobe. It differs markedly from small genomes of intracellular bacteria, retaining greater biosynthetic capabilities and lacking any evidence of extensive ongoing genome reduction. Comparative genomic microarray studies and bioinformatic analysis suggested that, despite its small size, almost 20% of the geno ...[more]

PMID: 17468768

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 - Dichelobacter nodosus (strain VCS1703A)

Publications

Genome sequence and identification of candidate vaccine antigens from the animal pathogen Dichelobacter nodosus.

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