Dataset Information

Whole Genome Metabolism - Comamonas testosteroni (strain CNB-2)

ABSTRACT:

Whole Genome Metabolism of "Comamonas testosteroni (strain CNB-2)"

This is a whole genome metabolism model of Comamonas testosteroni (strain CNB-2).

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: BMID000000141217 .

Other models with the same genus include BMID000000020368 BMID000000020369 BMID000000020370 BMID000000020371 BMID000000020372 BMID000000020373 BMID000000020374 BMID000000020375 BMID000000020376 BMID000000020377 BMID000000020378 BMID000000020379 BMID000000020380 BMID000000020381 BMID000000020382 BMID000000020383 BMID000000111148 BMID000000111149 BMID000000111150 BMID000000111151 BMID000000111152 BMID000000111153 BMID000000111154 BMID000000111155 BMID000000111156 BMID000000111157 BMID000000111158 BMID000000111159 BMID000000111160 BMID000000111161 BMID000000111162 BMID000000111163 BMID000000111164 BMID000000111165 BMID000000111166 BMID000000111167 BMID000000111168 BMID000000111169 BMID000000111170 BMID000000111171 BMID000000111172 BMID000000111173 BMID000000111174 BMID000000111175 BMID000000111176 BMID000000111177 BMID000000111178 BMID000000111179 BMID000000111180 BMID000000111181 BMID000000111182 BMID000000111183 BMID000000111184 BMID000000111185 BMID000000111186 BMID000000111187 BMID000000111188 BMID000000111189 BMID000000111190 BMID000000111191 BMID000000111192 BMID000000111193 BMID000000111194 BMID000000111195 BMID000000111196 BMID000000111197 BMID000000111198 BMID000000111199 BMID000000111200 BMID000000111201 BMID000000111202 BMID000000111203 BMID000000111204 BMID000000111205 BMID000000111206 BMID000000111207 BMID000000111208 BMID000000111209 BMID000000111210 BMID000000111211 BMID000000111212 BMID000000111213 BMID000000111214 BMID000000111215 BMID000000111216 BMID000000111217 BMID000000111218 BMID000000111219 BMID000000111220 BMID000000111221 BMID000000111222 BMID000000111223 BMID000000111224 BMID000000111225 BMID000000111226 BMID000000111227 BMID000000111228 BMID000000111229 BMID000000111230 BMID000000111231 BMID000000111232 BMID000000111233 BMID000000111234 BMID000000111235 BMID000000111236 .

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: BMID000000141217 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments.

Ma Ying-Fei YF Zhang Yun Y Zhang Jia-Yue JY Chen Dong-Wei DW Zhu Yongqian Y Zheng Huajun H Wang Sheng-Yue SY Jiang Cheng-Ying CY Zhao Guo-Ping GP Liu Shuang-Jiang SJ

Applied and environmental microbiology 20090904 21

Members of the gram-negative, strictly aerobic genus Comamonas occur in various environments. Here we report the complete genome of Comamonas testosteroni strain CNB-2. Strain CNB-2 has a circular chromosome that is 5,373,643 bp long and has a G+C content of 61.4%. A total of 4,803 open reading frames (ORFs) were identified; 3,514 of these ORFs are functionally assigned to energy production, cell growth, signal transduction, or transportation, while 866 ORFs encode hypothetical proteins and 423 ...[more]

PMID: 19734336

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 - Comamonas testosteroni (strain CNB-2)

Publications

The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments.

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