Dataset Information

Whole Genome Metabolism - Gluconobacter oxydans (strain 621H)

ABSTRACT:

Whole Genome Metabolism of "Gluconobacter oxydans (strain 621H)"

This is a whole genome metabolism model of Gluconobacter oxydans (strain 621H).

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: BMID000000140867 .

Other models with the same genus include BMID000000020134 BMID000000020135 BMID000000020136 BMID000000020137 BMID000000020138 BMID000000020139 BMID000000020140 BMID000000020141 BMID000000020142 BMID000000020143 BMID000000020144 BMID000000020145 BMID000000020146 BMID000000020147 BMID000000020148 BMID000000020149 BMID000000110256 BMID000000110257 BMID000000110258 BMID000000110259 BMID000000110260 BMID000000110261 BMID000000110262 BMID000000110263 BMID000000110264 BMID000000110265 BMID000000110266 BMID000000110267 BMID000000110268 BMID000000110269 BMID000000110270 BMID000000110271 BMID000000110272 BMID000000110273 BMID000000110274 BMID000000110275 BMID000000110276 BMID000000110277 BMID000000110278 BMID000000110279 BMID000000110280 BMID000000110281 BMID000000110282 BMID000000110283 BMID000000110284 BMID000000110285 BMID000000110286 BMID000000110287 BMID000000110288 BMID000000110289 BMID000000110290 BMID000000110291 BMID000000110292 BMID000000110293 BMID000000110294 BMID000000110295 BMID000000110296 BMID000000110297 BMID000000110298 BMID000000110299 BMID000000110300 BMID000000110301 BMID000000110302 BMID000000110303 BMID000000110304 BMID000000110305 BMID000000110306 BMID000000110307 BMID000000110308 BMID000000110309 BMID000000110310 BMID000000110311 BMID000000110312 BMID000000110313 BMID000000110314 BMID000000110315 BMID000000110316 BMID000000110317 BMID000000110318 BMID000000110319 BMID000000110320 BMID000000110321 BMID000000110322 BMID000000110323 BMID000000110324 BMID000000110325 BMID000000110326 BMID000000110327 BMID000000110328 BMID000000110329 BMID000000110330 BMID000000110331 BMID000000110332 BMID000000110333 BMID000000142172 .

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: BMID000000140867 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans.

Prust Christina C Hoffmeister Marc M Liesegang Heiko H Wiezer Arnim A Fricke Wolfgang Florian WF Ehrenreich Armin A Gottschalk Gerhard G Deppenmeier Uwe U

Nature biotechnology 20050123 2

Gluconobacter oxydans is unsurpassed by other organisms in its ability to incompletely oxidize a great variety of carbohydrates, alcohols and related compounds. Furthermore, the organism is used for several biotechnological processes, such as vitamin C production. To further our understanding of its overall metabolism, we sequenced the complete genome of G. oxydans 621H. The chromosome consists of 2,702,173 base pairs and contains 2,432 open reading frames. In addition, five plasmids were identi ...[more]

PMID: 15665824

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 - Gluconobacter oxydans (strain 621H)

Publications

Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans.

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