Dataset Information

Whole Genome Metabolism - Solibacter usitatus (strain Ellin6076)

ABSTRACT:

Whole Genome Metabolism of "Solibacter usitatus (strain Ellin6076)"

This is a whole genome metabolism model of Solibacter usitatus (strain Ellin6076).

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: BMID000000140853 .

Other models with the same genus include BMID000000017130 BMID000000017131 BMID000000017132 BMID000000017133 BMID000000017134 BMID000000017135 BMID000000017136 BMID000000017137 BMID000000017138 BMID000000017139 BMID000000017140 BMID000000017141 BMID000000017142 BMID000000017143 BMID000000017144 BMID000000017145 BMID000000098770 BMID000000098771 BMID000000098772 BMID000000098773 BMID000000098774 BMID000000098775 BMID000000098776 BMID000000098777 BMID000000098778 BMID000000098779 BMID000000098780 BMID000000098781 BMID000000098782 BMID000000098783 BMID000000098784 BMID000000098785 BMID000000098786 BMID000000098787 BMID000000098788 BMID000000098789 BMID000000098790 BMID000000098791 BMID000000098792 BMID000000098793 BMID000000098794 BMID000000098795 BMID000000098796 BMID000000098797 BMID000000098798 BMID000000098799 BMID000000098800 BMID000000098801 BMID000000098802 BMID000000098803 BMID000000098804 BMID000000098805 BMID000000098806 BMID000000098807 BMID000000098808 BMID000000098809 BMID000000098810 BMID000000098811 BMID000000098812 BMID000000098813 BMID000000098814 BMID000000098815 BMID000000098816 BMID000000098817 BMID000000098818 BMID000000098819 BMID000000098820 BMID000000098821 BMID000000098822 BMID000000098823 BMID000000098824 BMID000000098825 BMID000000098826 BMID000000098827 BMID000000098828 BMID000000098829 BMID000000098830 BMID000000098831 BMID000000098832 BMID000000098833 BMID000000098834 BMID000000098835 BMID000000098836 BMID000000098837 BMID000000098838 BMID000000098839 BMID000000098840 BMID000000098841 BMID000000098842 BMID000000098843 BMID000000098844 BMID000000098845 BMID000000098846 BMID000000098847 BMID000000098848 BMID000000098849 BMID000000098850 BMID000000098851 BMID000000098852 BMID000000098853 BMID000000098854 BMID000000098855 BMID000000098856 BMID000000098857 BMID000000098858 BMID000000098859 .

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: BMID000000140853 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Ward Naomi L NL Challacombe Jean F JF Janssen Peter H PH Henrissat Bernard B Coutinho Pedro M PM Wu Martin M Xie Gary G Haft Daniel H DH Sait Michelle M Badger Jonathan J Barabote Ravi D RD Bradley Brent B Brettin Thomas S TS Brinkac Lauren M LM Bruce David D Creasy Todd T Daugherty Sean C SC Davidsen Tanja M TM DeBoy Robert T RT Detter J Chris JC Dodson Robert J RJ Durkin A Scott AS Ganapathy Anuradha A Gwinn-Giglio Michelle M Han Cliff S CS Khouri Hoda H Kiss Hajnalka H Kothari Sagar P SP Madupu Ramana R Nelson Karen E KE Nelson William C WC Paulsen Ian I Penn Kevin K Ren Qinghu Q Rosovitz M J MJ Selengut Jeremy D JD Shrivastava Susmita S Sullivan Steven A SA Tapia Roxanne R Thompson L Sue LS Watkins Kisha L KL Yang Qi Q Yu Chunhui C Zafar Nikhat N Zhou Liwei L Kuske Cheryl R CR

Applied and environmental microbiology 20090205 7

The complete genomes of three strains from the phylum Acidobacteria were compared. Phylogenetic analysis placed them as a unique phylum. They share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi. The three strains appear to be versatile heterotrophs. Genomic and culture traits indicate the use of carbon sources that span simple sugars to more complex substrates such as hemicellulose, cellulose, and chitin. The genomes encode low-specificity major facilitator ...[more]

PMID: 19201974

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 - Solibacter usitatus (strain Ellin6076)

Publications

Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets