Dataset Information

Whole Genome Metabolism - Shigella sonnei (strain Ss046)

ABSTRACT:

Whole Genome Metabolism of "Shigella sonnei (strain Ss046)"

This is a whole genome metabolism model of Shigella sonnei (strain Ss046).

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: BMID000000140468 .

Other models with the same genus include BMID000000000493 BMID000000000494 BMID000000000495 BMID000000000496 BMID000000000497 BMID000000000498 BMID000000000499 BMID000000000500 BMID000000000501 BMID000000000502 BMID000000000503 BMID000000000504 BMID000000000505 BMID000000000506 BMID000000000507 BMID000000000508 BMID000000000509 BMID000000029415 BMID000000029416 BMID000000029417 BMID000000029418 BMID000000029419 BMID000000029420 BMID000000029421 BMID000000029422 BMID000000029423 BMID000000029424 BMID000000029425 BMID000000029426 BMID000000029427 BMID000000029428 BMID000000029429 BMID000000029430 BMID000000029431 BMID000000029432 BMID000000029433 BMID000000029434 BMID000000029435 BMID000000029436 BMID000000029437 BMID000000029438 BMID000000029439 BMID000000029440 BMID000000029441 BMID000000029442 BMID000000029443 BMID000000029444 BMID000000029445 BMID000000029446 BMID000000029447 BMID000000029448 BMID000000029449 BMID000000029450 BMID000000029451 BMID000000029452 BMID000000029453 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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: BMID000000140468 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.

Yang Fan F Yang Jian J Zhang Xiaobing X Chen Lihong L Jiang Yan Y Yan Yongliang Y Tang Xudong X Wang Jing J Xiong Zhaohui Z Dong Jie J Xue Ying Y Zhu Yafang Y Xu Xingye X Sun Lilian L Chen Shuxia S Nie Huan H Peng Junping J Xu Jianguo J Wang Yu Y Yuan Zhenghong Z Wen Yumei Y Yao Zhijian Z Shen Yan Y Qiang Boqin B Hou Yunde Y Yu Jun J Jin Qi Q

Nucleic acids research 20051107 19

The Shigella bacteria cause bacillary dysentery, which remains a significant threat to public health. The genus status and species classification appear no longer valid, as compelling evidence indicates that Shigella, as well as enteroinvasive Escherichia coli, are derived from multiple origins of E.coli and form a single pathovar. Nevertheless, Shigella dysenteriae serotype 1 causes deadly epidemics but Shigella boydii is restricted to the Indian subcontinent, while Shigella flexneri and Shigel ...[more]

PMID: 16275786

Publication: 1/3

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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 - Shigella sonnei (strain Ss046)

Publications

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery.

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