Dataset Information

Whole Genome Metabolism - Pseudoxanthomonas spadix (strain BD-a59)

ABSTRACT:

Whole Genome Metabolism of "Pseudoxanthomonas spadix (strain BD-a59)"

This is a whole genome metabolism model of Pseudoxanthomonas spadix (strain BD-a59).

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: BMID000000141005 .

Other models with the same genus include BMID000000003947 BMID000000003948 BMID000000003949 BMID000000003950 BMID000000003951 BMID000000003952 BMID000000003953 BMID000000003954 BMID000000003955 BMID000000003956 BMID000000003957 BMID000000003958 BMID000000003959 BMID000000003960 BMID000000003961 BMID000000003962 BMID000000003963 BMID000000044249 BMID000000044250 BMID000000044251 BMID000000044252 BMID000000044253 BMID000000044254 BMID000000044255 BMID000000044256 BMID000000044257 BMID000000044258 BMID000000044259 BMID000000044260 BMID000000044261 BMID000000044262 BMID000000044263 BMID000000044264 BMID000000044265 BMID000000044266 BMID000000044267 BMID000000044268 BMID000000044269 BMID000000044270 BMID000000044271 BMID000000044272 BMID000000044273 BMID000000044274 BMID000000044275 BMID000000044276 BMID000000044277 BMID000000044278 BMID000000044279 BMID000000044280 BMID000000044281 BMID000000044282 BMID000000044283 BMID000000044284 BMID000000044285 BMID000000044286 BMID000000044287 BMID000000044288 BMID000000044289 BMID000000044290 BMID000000044291 BMID000000044292 BMID000000044293 BMID000000044294 BMID000000044295 BMID000000044296 BMID000000044297 BMID000000044298 BMID000000044299 BMID000000044300 BMID000000044301 BMID000000044302 BMID000000044303 BMID000000044304 BMID000000044305 BMID000000044306 BMID000000044307 BMID000000044308 BMID000000044309 BMID000000044310 BMID000000044311 BMID000000044312 BMID000000044313 BMID000000044314 BMID000000044315 BMID000000044316 BMID000000044317 BMID000000044318 BMID000000044319 BMID000000044320 BMID000000044321 BMID000000044322 BMID000000044323 BMID000000044324 BMID000000044325 BMID000000044326 BMID000000044327 BMID000000044328 BMID000000044329 BMID000000044330 BMID000000044331 BMID000000044332 BMID000000044333 BMID000000141659 .

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: BMID000000141005 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59.

Lee Seung Hyeon SH Jin Hyun Mi HM Lee Hyo Jung HJ Kim Jeong Myeong JM Jeon Che Ok CO

Journal of bacteriology 20120101 2

Pseudoxanthomonas spadix BD-a59, able to metabolize all six BTEX (benzene, toluene, ethylbenzene, and o-, m-, and p-xylene) compounds, was isolated from gasoline-contaminated sediment. Here, we report the complete 3.45-Mb genome sequence and annotation of strain BD-a59. These advance the understanding of strain BD-a59's genomic properties and pollutant metabolic versatility. ...[more]

PMID: 22207748

Publication: 1/2

Similar Datasets

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 - Pseudoxanthomonas spadix (strain BD-a59)

Publications

Complete genome sequence of the BTEX-degrading bacterium Pseudoxanthomonas spadix BD-a59.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets