Dataset Information

Whole Genome Metabolism - Xylella fastidiosa (strain M23)

ABSTRACT:

Whole Genome Metabolism of "Xylella fastidiosa (strain M23)"

This is a whole genome metabolism model of Xylella fastidiosa (strain M23).

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: BMID000000141017 .

Other models with the same genus include BMID000000006613 BMID000000006614 BMID000000006615 BMID000000006616 BMID000000006617 BMID000000006618 BMID000000006619 BMID000000006620 BMID000000006621 BMID000000006622 BMID000000006623 BMID000000006624 BMID000000006625 BMID000000006626 BMID000000055269 BMID000000055270 BMID000000055271 BMID000000055272 BMID000000055273 BMID000000055274 BMID000000055275 BMID000000055276 BMID000000055277 BMID000000055278 BMID000000055279 BMID000000055280 BMID000000055281 BMID000000055282 BMID000000055283 BMID000000055284 BMID000000055285 BMID000000055286 BMID000000055287 BMID000000055288 BMID000000055289 BMID000000055290 BMID000000055291 BMID000000055292 BMID000000055293 BMID000000055294 BMID000000055295 BMID000000055296 BMID000000055297 BMID000000055298 BMID000000055299 BMID000000055300 BMID000000055301 BMID000000055302 BMID000000055303 BMID000000055304 BMID000000055305 BMID000000055306 BMID000000055307 BMID000000055308 BMID000000055309 BMID000000055310 BMID000000055311 BMID000000055312 BMID000000055313 BMID000000055314 BMID000000055315 BMID000000055316 BMID000000055317 BMID000000055318 BMID000000055319 BMID000000055320 BMID000000055321 BMID000000055322 BMID000000055323 BMID000000055324 BMID000000055325 BMID000000055326 BMID000000055327 BMID000000055328 BMID000000055329 BMID000000055330 BMID000000055331 BMID000000055332 BMID000000055333 BMID000000055334 BMID000000055335 BMID000000055336 BMID000000055337 BMID000000055338 BMID000000055339 BMID000000055340 BMID000000055341 BMID000000141056 BMID000000006966 BMID000000006967 BMID000000006968 BMID000000006969 BMID000000006970 BMID000000006971 BMID000000006972 BMID000000006973 BMID000000006974 BMID000000006975 BMID000000006976 BMID000000006977 BMID000000006978 BMID000000006979 BMID000000056970 BMID000000056971 BMID000000056972 BMID000000056973 BMID000000056974 BMID000000056975 BMID000000056976 BMID000000056977 BMID000000056978 BMID000000056979 BMID000000056980 BMID000000056981 BMID000000056982 BMID000000056983 BMID000000056984 BMID000000056985 BMID000000056986 BMID000000056987 BMID000000056988 BMID000000056989 BMID000000056990 BMID000000056991 BMID000000056992 BMID000000056993 BMID000000056994 BMID000000056995 BMID000000056996 BMID000000056997 BMID000000056998 BMID000000056999 BMID000000057000 BMID000000057001 BMID000000057002 BMID000000057003 BMID000000057004 BMID000000057005 BMID000000057006 BMID000000057007 BMID000000057008 BMID000000057009 BMID000000057010 BMID000000057011 BMID000000057012 BMID000000057013 BMID000000057014 BMID000000057015 BMID000000057016 BMID000000057017 BMID000000057018 BMID000000057019 BMID000000057020 BMID000000057021 BMID000000057022 BMID000000057023 BMID000000057024 BMID000000057025 BMID000000057026 BMID000000057027 BMID000000057028 BMID000000057029 BMID000000057030 BMID000000057031 BMID000000057032 BMID000000057033 BMID000000057034 BMID000000057035 BMID000000057036 BMID000000057037 BMID000000057038 BMID000000057039 BMID000000057040 BMID000000057041 BMID000000141229 BMID000000015918 BMID000000015919 BMID000000015920 BMID000000015921 BMID000000015922 BMID000000015923 BMID000000015924 BMID000000015925 BMID000000015926 BMID000000015927 BMID000000015928 BMID000000015929 BMID000000015930 BMID000000015931 BMID000000093942 BMID000000093943 BMID000000093944 BMID000000093945 BMID000000093946 BMID000000093947 BMID000000093948 BMID000000093949 BMID000000093950 BMID000000093951 BMID000000093952 BMID000000093953 BMID000000093954 BMID000000093955 BMID000000093956 BMID000000093957 BMID000000093958 BMID000000093959 BMID000000093960 BMID000000093961 BMID000000093962 BMID000000093963 BMID000000093964 BMID000000093965 BMID000000093966 BMID000000093967 BMID000000093968 BMID000000093969 BMID000000093970 BMID000000093971 BMID000000093972 BMID000000093973 BMID000000093974 BMID000000093975 BMID000000093976 BMID000000093977 BMID000000093978 BMID000000093979 BMID000000093980 BMID000000093981 BMID000000093982 BMID000000093983 BMID000000093984 BMID000000093985 BMID000000093986 BMID000000093987 BMID000000093988 BMID000000093989 BMID000000093990 BMID000000093991 BMID000000093992 BMID000000093993 BMID000000093994 BMID000000093995 BMID000000093996 BMID000000093997 BMID000000093998 BMID000000093999 BMID000000094000 BMID000000094001 BMID000000094002 BMID000000094003 BMID000000094004 BMID000000094005 BMID000000094006 BMID000000094007 BMID000000094008 BMID000000094009 BMID000000094010 BMID000000094011 BMID000000094012 BMID000000094013 BMID000000020341 BMID000000020342 BMID000000020343 BMID000000020344 BMID000000020345 BMID000000020346 BMID000000020347 BMID000000020348 BMID000000020349 BMID000000020350 BMID000000020351 BMID000000020352 BMID000000020353 BMID000000020354 BMID000000111010 BMID000000111011 BMID000000111012 BMID000000111013 BMID000000111014 BMID000000111015 BMID000000111016 BMID000000111017 BMID000000111018 BMID000000111019 BMID000000111020 BMID000000111021 BMID000000111022 BMID000000111023 BMID000000111024 BMID000000111025 BMID000000111026 BMID000000111027 BMID000000111028 BMID000000111029 BMID000000111030 BMID000000111031 BMID000000111032 BMID000000111033 BMID000000111034 BMID000000111035 BMID000000111036 BMID000000111037 BMID000000111038 BMID000000111039 BMID000000111040 BMID000000111041 BMID000000111042 BMID000000111043 BMID000000111044 BMID000000111045 BMID000000111046 BMID000000111047 BMID000000111048 BMID000000111049 BMID000000111050 BMID000000111051 BMID000000111052 BMID000000111053 BMID000000111054 BMID000000111055 BMID000000111056 BMID000000111057 BMID000000111058 BMID000000111059 BMID000000111060 BMID000000111061 BMID000000111062 BMID000000111063 BMID000000111064 BMID000000111065 BMID000000111066 BMID000000111067 BMID000000111068 BMID000000111069 BMID000000111070 BMID000000111071 BMID000000111072 BMID000000111073 BMID000000111074 BMID000000111075 BMID000000111076 BMID000000111077 BMID000000111078 BMID000000111079 BMID000000111080 BMID000000111081 BMID000000111082 BMID000000111083 BMID000000141977 BMID000000142089 .

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: BMID000000141017 | biostudies-other |

SECONDARY ACCESSION(S): 24180668

REPOSITORIES: biostudies-other

ACCESS DATA

Publications

Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel Finja F Rodriguez Nicolas N Swainston Neil N Wrzodek Clemens C Wrzodek Clemens C Czauderna Tobias T Keller Roland R Mittag Florian F Schubert Michael M Glont Mihai M Golebiewski Martin M van Iersel Martijn M Keating Sarah S Rall Matthias M Wybrow Michael M Hermjakob Henning H Hucka Michael M Kell Douglas B DB Müller Wolfgang W Mendes Pedro P Zell Andreas A Chaouiya Claudine C Saez-Rodriguez Julio J Schreiber Falk F Laibe Camille C Dräger Andreas A Le Novère Nicolas N

BMC systems biology 20131101

<h4>Background</h4>Systems biology projects and omics technologies have led to a growing number of biochemical pathway models and reconstructions. However, the majority of these models are still created de novo, based on literature mining and the manual processing of pathway data.<h4>Results</h4>To increase the efficiency of model creation, the Path2Models project has automatically generated mathematical models from pathway representations using a suite of freely available software. Data sources ...[more]

PMID: 24180668

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 - Xylella fastidiosa (strain M23)

Publications

Path2Models: large-scale generation of computational models from biochemical pathway maps.

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