Dataset Information

Whole Genome Metabolism - Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)

ABSTRACT:

Whole Genome Metabolism of "Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)"

This is a whole genome metabolism model of Cryptococcus neoformans var. neoformans serotype D (strain B-3501A).

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: BMID000000141997 .

Other models with the same genus include BMID000000002213 BMID000000002214 BMID000000002215 BMID000000002216 BMID000000002217 BMID000000002218 BMID000000002219 BMID000000002220 BMID000000002221 BMID000000002222 BMID000000002223 BMID000000002224 BMID000000002225 BMID000000002226 BMID000000002227 BMID000000002228 BMID000000002229 BMID000000002230 BMID000000002231 BMID000000002232 BMID000000002233 BMID000000002234 BMID000000002235 BMID000000002236 BMID000000002237 BMID000000002238 BMID000000002239 BMID000000002240 BMID000000002241 BMID000000002242 BMID000000037363 BMID000000037364 BMID000000037365 BMID000000037366 BMID000000037367 BMID000000037368 BMID000000037369 BMID000000037370 BMID000000037371 BMID000000037372 BMID000000037373 BMID000000037374 BMID000000037375 BMID000000037376 BMID000000037377 BMID000000037378 BMID000000037379 BMID000000037380 BMID000000037381 BMID000000037382 BMID000000037383 BMID000000037384 BMID000000037385 BMID000000037386 BMID000000037387 BMID000000037388 BMID000000037389 BMID000000037390 BMID000000037391 BMID000000037392 BMID000000037393 BMID000000037394 BMID000000037395 BMID000000037396 BMID000000037397 BMID000000037398 BMID000000037399 BMID000000037400 BMID000000037401 BMID000000037402 BMID000000037403 BMID000000037404 BMID000000037405 BMID000000037406 BMID000000037407 BMID000000037408 BMID000000037409 BMID000000037410 BMID000000037411 BMID000000037412 BMID000000037413 BMID000000037414 BMID000000037415 BMID000000037416 BMID000000037417 BMID000000037418 BMID000000037419 BMID000000037420 BMID000000037421 BMID000000037422 BMID000000037423 BMID000000037424 BMID000000037425 BMID000000037426 BMID000000037427 BMID000000037428 BMID000000037429 BMID000000037430 BMID000000037431 BMID000000037432 BMID000000037433 BMID000000037434 BMID000000021677 BMID000000021678 BMID000000021679 BMID000000021680 BMID000000021681 BMID000000021682 BMID000000021683 BMID000000021684 BMID000000021685 BMID000000021686 BMID000000021687 BMID000000021688 BMID000000021689 BMID000000021690 BMID000000021691 BMID000000021692 BMID000000021693 BMID000000021694 BMID000000021695 BMID000000021696 BMID000000021697 BMID000000021698 BMID000000021699 BMID000000021700 BMID000000021701 BMID000000021702 BMID000000021703 BMID000000021704 BMID000000021705 BMID000000021706 BMID000000117104 BMID000000117105 BMID000000117106 BMID000000117107 BMID000000117108 BMID000000117109 BMID000000117110 BMID000000117111 BMID000000117112 BMID000000117113 BMID000000117114 BMID000000117115 BMID000000117116 BMID000000117117 BMID000000117118 BMID000000117119 BMID000000117120 BMID000000117121 BMID000000117122 BMID000000117123 BMID000000117124 BMID000000117125 BMID000000117126 BMID000000117127 BMID000000117128 BMID000000117129 BMID000000117130 BMID000000117131 BMID000000117132 BMID000000117133 BMID000000117134 BMID000000117135 BMID000000117136 BMID000000117137 BMID000000117138 BMID000000117139 BMID000000117140 BMID000000117141 BMID000000117142 BMID000000117143 BMID000000117144 BMID000000117145 BMID000000117146 BMID000000117147 BMID000000117148 BMID000000117149 BMID000000117150 BMID000000117151 BMID000000117152 BMID000000117153 BMID000000117154 BMID000000117155 BMID000000117156 BMID000000117157 BMID000000117158 BMID000000117159 BMID000000117160 BMID000000117161 BMID000000117162 BMID000000117163 BMID000000117164 BMID000000117165 BMID000000117166 BMID000000117167 BMID000000117168 BMID000000117169 BMID000000117170 BMID000000117171 BMID000000117172 BMID000000117173 BMID000000117174 BMID000000117175 BMID000000140372 BMID000000142614 .

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: BMID000000141997 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

Loftus Brendan J BJ Fung Eula E Roncaglia Paola P Rowley Don D Amedeo Paolo P Bruno Dan D Vamathevan Jessica J Miranda Molly M Anderson Iain J IJ Fraser James A JA Allen Jonathan E JE Bosdet Ian E IE Brent Michael R MR Chiu Readman R Doering Tamara L TL Donlin Maureen J MJ D'Souza Cletus A CA Fox Deborah S DS Grinberg Viktoriya V Fu Jianmin J Fukushima Marilyn M Haas Brian J BJ Huang James C JC Janbon Guilhem G Jones Steven J M SJ Koo Hean L HL Krzywinski Martin I MI Kwon-Chung June K JK Lengeler Klaus B KB Maiti Rama R Marra Marco A MA Marra Robert E RE Mathewson Carrie A CA Mitchell Thomas G TG Pertea Mihaela M Riggs Florenta R FR Salzberg Steven L SL Schein Jacqueline E JE Shvartsbeyn Alla A Shin Heesun H Shumway Martin M Specht Charles A CA Suh Bernard B BB Tenney Aaron A Utterback Terry R TR Wickes Brian L BL Wortman Jennifer R JR Wye Natasja H NH Kronstad James W JW Lodge Jennifer K JK Heitman Joseph J Davis Ronald W RW Fraser Claire M CM Hyman Richard W RW

Science (New York, N.Y.) 20050113 5713

Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its approximately 20-megabase genome, which contains approximately 6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposon ...[more]

PMID: 15653466

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 - Cryptococcus neoformans var. neoformans serotype D (strain B-3501A)

Publications

The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans.

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