Dataset Information

Whole Genome Metabolism - Microbacterium testaceum (strain StLB037)

ABSTRACT:

Whole Genome Metabolism of "Microbacterium testaceum (strain StLB037)"

This is a whole genome metabolism model of Microbacterium testaceum (strain StLB037).

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: BMID000000141748 .

Other models with the same genus include BMID000000008139 BMID000000008140 BMID000000008141 BMID000000008142 BMID000000008143 BMID000000008144 BMID000000008145 BMID000000008146 BMID000000008147 BMID000000008148 BMID000000008149 BMID000000008150 BMID000000008151 BMID000000008152 BMID000000008153 BMID000000008154 BMID000000062371 BMID000000062372 BMID000000062373 BMID000000062374 BMID000000062375 BMID000000062376 BMID000000062377 BMID000000062378 BMID000000062379 BMID000000062380 BMID000000062381 BMID000000062382 BMID000000062383 BMID000000062384 BMID000000062385 BMID000000062386 BMID000000062387 BMID000000062388 BMID000000062389 BMID000000062390 BMID000000062391 BMID000000062392 BMID000000062393 BMID000000062394 BMID000000062395 BMID000000062396 BMID000000062397 BMID000000062398 BMID000000062399 BMID000000062400 BMID000000062401 BMID000000062402 BMID000000062403 BMID000000062404 BMID000000062405 BMID000000062406 BMID000000062407 BMID000000062408 BMID000000062409 BMID000000062410 BMID000000062411 BMID000000062412 BMID000000062413 BMID000000062414 BMID000000062415 BMID000000062416 BMID000000062417 BMID000000062418 BMID000000062419 BMID000000062420 BMID000000062421 BMID000000062422 BMID000000062423 BMID000000062424 BMID000000062425 BMID000000062426 BMID000000062427 BMID000000062428 BMID000000062429 BMID000000062430 BMID000000062431 BMID000000062432 BMID000000062433 BMID000000062434 BMID000000062435 BMID000000062436 BMID000000062437 BMID000000062438 BMID000000062439 BMID000000062440 BMID000000062441 BMID000000062442 BMID000000062443 BMID000000062444 BMID000000062445 BMID000000062446 BMID000000062447 BMID000000062448 BMID000000062449 BMID000000062450 BMID000000062451 BMID000000062452 BMID000000062453 BMID000000062454 BMID000000062455 BMID000000062456 .

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: BMID000000141748 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome sequence of Microbacterium testaceum StLB037, an N-acylhomoserine lactone-degrading bacterium isolated from potato leaves.

Morohoshi Tomohiro T Wang Wen-Zhao WZ Someya Nobutaka N Ikeda Tsukasa T

Journal of bacteriology 20110225 8

Microbacterium testaceum is an endophytic Gram-positive bacterium that resides within plant hosts. M. testaceum StLB037 was isolated from potato leaves and shows N-acylhomoserine lactone-degrading activity. Here, we present the 3.98-Mb complete genome sequence of StLB037, with an average GC content of 70.28%. ...[more]

PMID: 21357489

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 - Microbacterium testaceum (strain StLB037)

Publications

Genome sequence of Microbacterium testaceum StLB037, an N-acylhomoserine lactone-degrading bacterium isolated from potato leaves.

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