Dataset Information

Whole Genome Metabolism - Cyanidioschyzon merolae strain 10D

ABSTRACT:

Whole Genome Metabolism of "Cyanidioschyzon merolae strain 10D"

This is a whole genome metabolism model of Cyanidioschyzon merolae strain 10D.

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: BMID000000141432 .

Other models with the same genus include BMID000000013817 BMID000000013818 BMID000000013819 BMID000000013820 BMID000000013821 BMID000000013822 BMID000000013823 BMID000000013824 BMID000000013825 BMID000000013826 BMID000000013827 BMID000000013828 BMID000000013829 BMID000000013830 BMID000000013831 BMID000000013832 BMID000000013833 BMID000000013834 BMID000000013835 BMID000000013836 BMID000000013837 BMID000000013838 BMID000000013839 BMID000000013840 BMID000000013841 BMID000000013842 BMID000000013843 BMID000000084939 BMID000000084940 BMID000000084941 BMID000000084942 BMID000000084943 BMID000000084944 BMID000000084945 BMID000000084946 BMID000000084947 BMID000000084948 BMID000000084949 BMID000000084950 BMID000000084951 BMID000000084952 BMID000000084953 BMID000000084954 BMID000000084955 BMID000000084956 BMID000000084957 BMID000000084958 BMID000000084959 BMID000000084960 BMID000000084961 BMID000000084962 BMID000000084963 BMID000000084964 BMID000000084965 BMID000000084966 BMID000000084967 BMID000000084968 BMID000000084969 BMID000000084970 BMID000000084971 BMID000000084972 BMID000000084973 BMID000000084974 BMID000000084975 BMID000000084976 BMID000000084977 BMID000000084978 BMID000000084979 BMID000000084980 BMID000000084981 BMID000000084982 BMID000000084983 BMID000000084984 BMID000000084985 BMID000000084986 BMID000000084987 BMID000000084988 BMID000000084989 BMID000000084990 BMID000000084991 BMID000000084992 BMID000000084993 BMID000000084994 BMID000000084995 BMID000000084996 BMID000000084997 BMID000000084998 BMID000000084999 BMID000000085000 BMID000000085001 BMID000000085002 BMID000000085003 BMID000000085004 BMID000000085005 BMID000000085006 BMID000000085007 BMID000000085008 BMID000000085009 BMID000000085010 BMID000000085011 BMID000000085012 .

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: BMID000000141432 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.

Matsuzaki Motomichi M Misumi Osami O Shin-I Tadasu T Maruyama Shinichiro S Takahara Manabu M Miyagishima Shin-Ya SY Mori Toshiyuki T Nishida Keiji K Yagisawa Fumi F Nishida Keishin K Yoshida Yamato Y Nishimura Yoshiki Y Nakao Shunsuke S Kobayashi Tamaki T Momoyama Yu Y Higashiyama Tetsuya T Minoda Ayumi A Sano Masako M Nomoto Hisayo H Oishi Kazuko K Hayashi Hiroko H Ohta Fumiko F Nishizaka Satoko S Haga Shinobu S Miura Sachiko S Morishita Tomomi T Kabeya Yukihiro Y Terasawa Kimihiro K Suzuki Yutaka Y Ishii Yasuyuki Y Asakawa Shuichi S Takano Hiroyoshi H Ohta Niji N Kuroiwa Haruko H Tanaka Kan K Shimizu Nobuyoshi N Sugano Sumio S Sato Naoki N Nozaki Hisayoshi H Ogasawara Naotake N Kohara Yuji Y Kuroiwa Tsuneyoshi T

Nature 20040401 6983

Small, compact genomes of ultrasmall unicellular algae provide information on the basic and essential genes that support the lives of photosynthetic eukaryotes, including higher plants. Here we report the 16,520,305-base-pair sequence of the 20 chromosomes of the unicellular red alga Cyanidioschyzon merolae 10D as the first complete algal genome. We identified 5,331 genes in total, of which at least 86.3% were expressed. Unique characteristics of this genomic structure include: a lack of introns ...[more]

PMID: 15071595

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 - Cyanidioschyzon merolae strain 10D

Publications

Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D.

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