Dataset Information

Whole Genome Metabolism - Thermosipho africanus (strain TCF52B)

ABSTRACT:

Whole Genome Metabolism of "Thermosipho africanus (strain TCF52B)"

This is a whole genome metabolism model of Thermosipho africanus (strain TCF52B).

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: BMID000000140764 .

Other models with the same genus include BMID000000001485 BMID000000001486 BMID000000001487 BMID000000001488 BMID000000001489 BMID000000001490 BMID000000001491 BMID000000001492 BMID000000001493 BMID000000001494 BMID000000001495 BMID000000001496 BMID000000001497 BMID000000001498 BMID000000001499 BMID000000034068 BMID000000034069 BMID000000034070 BMID000000034071 BMID000000034072 BMID000000034073 BMID000000034074 BMID000000034075 BMID000000034076 BMID000000034077 BMID000000034078 BMID000000034079 BMID000000034080 BMID000000034081 BMID000000034082 BMID000000034083 BMID000000034084 BMID000000034085 BMID000000034086 BMID000000034087 BMID000000034088 BMID000000034089 BMID000000034090 BMID000000034091 BMID000000034092 BMID000000034093 BMID000000034094 BMID000000034095 BMID000000034096 BMID000000034097 BMID000000034098 BMID000000034099 BMID000000034100 BMID000000034101 BMID000000034102 BMID000000034103 BMID000000034104 BMID000000034105 BMID000000034106 BMID000000034107 BMID000000034108 BMID000000034109 BMID000000034110 BMID000000034111 BMID000000034112 BMID000000034113 BMID000000034114 BMID000000034115 BMID000000034116 BMID000000034117 BMID000000034118 BMID000000034119 BMID000000034120 BMID000000034121 BMID000000034122 BMID000000034123 BMID000000034124 BMID000000034125 BMID000000034126 BMID000000034127 BMID000000034128 BMID000000034129 BMID000000034130 BMID000000034131 BMID000000034132 BMID000000034133 BMID000000034134 BMID000000034135 BMID000000034136 BMID000000141767 BMID000000022555 BMID000000022556 BMID000000022557 BMID000000022558 BMID000000022559 BMID000000022560 BMID000000022561 BMID000000022562 BMID000000022563 BMID000000022564 BMID000000022565 BMID000000022566 BMID000000022567 BMID000000022568 BMID000000022569 BMID000000121134 BMID000000121135 BMID000000121136 BMID000000121137 BMID000000121138 BMID000000121139 BMID000000121140 BMID000000121141 BMID000000121142 BMID000000121143 BMID000000121144 BMID000000121145 BMID000000121146 BMID000000121147 BMID000000121148 BMID000000121149 BMID000000121150 BMID000000121151 BMID000000121152 BMID000000121153 BMID000000121154 BMID000000121155 BMID000000121156 BMID000000121157 BMID000000121158 BMID000000121159 BMID000000121160 BMID000000121161 BMID000000121162 BMID000000121163 BMID000000121164 BMID000000121165 BMID000000121166 BMID000000121167 BMID000000121168 BMID000000121169 BMID000000121170 BMID000000121171 BMID000000121172 BMID000000121173 BMID000000121174 BMID000000121175 BMID000000121176 BMID000000121177 BMID000000121178 BMID000000121179 BMID000000121180 BMID000000121181 BMID000000121182 BMID000000121183 BMID000000121184 BMID000000121185 BMID000000121186 BMID000000121187 BMID000000121188 BMID000000121189 BMID000000121190 BMID000000121191 BMID000000121192 BMID000000121193 BMID000000121194 BMID000000121195 BMID000000121196 BMID000000121197 BMID000000121198 BMID000000121199 BMID000000121200 BMID000000121201 BMID000000121202 BMID000000121203 BMID000000121204 .

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: BMID000000140764 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

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Publications

The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.

Nesbø Camilla L CL Bapteste Eric E Curtis Bruce B Dahle Håkon H Lopez Philippe P Macleod Dave D Dlutek Marlena M Bowman Sharen S Zhaxybayeva Olga O Birkeland Nils-Kåre NK Doolittle W Ford WF

Journal of bacteriology 20090105 6

Lateral gene transfers (LGT) (also called horizontal gene transfers) have been a major force shaping the Thermosipho africanus TCF52B genome, whose sequence we describe here. Firmicutes emerge as the principal LGT partner. Twenty-six percent of phylogenetic trees suggest LGT with this group, while 13% of the open reading frames indicate LGT with Archaea. ...[more]

PMID: 19124572

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 - Thermosipho africanus (strain TCF52B)

Publications

The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea.

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