An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

Nucleic Acids Research

Volumn 42, Issue 22, 2014, Pages 13525-13533

  Bock, Thomas ^a   Chen, Wei Hua ^a,d   Ori, Alessandro ^a   Malik, Nayab ^a,e   Silva Martin, Noella ^a   Huerta Cepas, Jaime ^a   Powell, Sean T ^a   Kastritis, Panagiotis L ^a   Smyshlyaev, Georgy ^a,b   Vonkova, Ivana ^a   Kirkpatrick, Joanna ^a   Doerks, Tobias ^a   Nesme, Leo ^a   Baßler, Jochen ^c   Kos, Martin ^c   Hurt, Ed ^c   Carlomagno, Teresa ^a   Gavin, Anne Claude ^a   Barabas, Orsolya ^a   Müller, Christoph W ^a   Noort, Vera Van ^a,f   Beck, Martin ^a   Bork, Peer ^a   more..

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

^c UNIVERSITY OF HEIDELBERG   (Germany)

^d UNIVERSITY OF GENEVA   (Switzerland)

^e TRINITY COLLEGE   (United Kingdom)

^f UNIVERSITY OF LEUVEN   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEOME; FUNGAL PROTEIN; TRANSCRIPTOME;

ALTERNATIVE RNA SPLICING; AMINO TERMINAL SEQUENCE; ARTICLE; CARBOXY TERMINAL SEQUENCE; CHAETOMIUM; CHAETOMIUM THERMOPHILUM; CT GENE; FUNGAL GENE; GENE EXPRESSION; GENE STRUCTURE; GENOME ANALYSIS; INTRON; LONG TERMINAL REPEAT; MESOPHILE; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; RNA SEQUENCE; RNA TRANSLATION; STOP CODON; TANDEM REPEAT; TRANSPOSON; FUNGAL GENOME; GENETICS; METABOLISM; MOLECULAR GENETICS; PSEUDOGENE;

CHAETOMIUM THERMOPHILUM; EUKARYOTA; FUNGI;

CHAETOMIUM; FUNGAL PROTEINS; GENES, FUNGAL; GENOME, FUNGAL; INTRONS; MOLECULAR SEQUENCE ANNOTATION; PROTEOME; PSEUDOGENES; TRANSCRIPTOME;

EID: 84927669907     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1147     Document Type: Article

References (35)

1. Perutz, M. F. and Raidt, H. (1975) Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2. Nature, 255, 256-259.
2. Perutz, M. F. (1978) Electrostatic effects in proteins. Science, 201, 1187-1191.
3. Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D. P., Arumugam, M., Bork, P. and Hurt, E. (2011) Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell, 146, 277-289.
4. Thierbach, K., von Appen, A., Thoms, M., Beck, M., Flemming, D. and Hurt, E. (2013) Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy. Structure, 21, 1672-1682.
5. Monecke, T., Haselbach, D., Voß, B., Russek, A., Neumann, P., Thomson, E., Hurt, E., Zachariae, U., Stark, H., Grubmüller, H. et al. (2013) Structural basis for cooperativity of CRM1 export complex formation. Proc. Natl Acad. Sci. U. S. A., 110, 960-965.
6. Leidig, C., Bange, G., Kopp, J. U. R., Amlacher, S., Aravind, A., Wickles, S., Witte, G., Hurt, E., Beckmann, R. and Sinning, I. (2012) Structural characterization of a eukaryotic chaperone - the ribosome-associated complex. Nat. Struct. Mol. Biol., 20, 23-28.
7. Hondele, M., Stuwe, T., Hassler, M., Halbach, F., Bowman, A., Zhang, E. T., Nijmeijer, B., Kotthoff, C., Rybin, V., Amlacher, S. et al. (2013) Structural basis of histone H2A-H2B recognition by the essential chaperone FACT. Nature, 499, 111-114.
8. Lapinaite, A., Simon, B., Skjaerven, L., Rakwalska-Bange, M., Gabel, F. and Carlomagno, T. (2013) The structure of the box C/D enzyme reveals regulation of RNA methylation. Nature, 502, 519-523.
9. Mathé, C., Sagot, M.-F., Schiex, T. and Rouzé, P. (2002) Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res., 30, 4103-4117.
10. Langmead, B. and Salzberg, S. L. (2012) Fast gapped-read alignment with Bowtie 2. Nat. Methods, 9, 357-359.
11. Ori, A., Banterle, N., Iskar, M., Andrés-Pons, A., Escher, C., Khanh Bui, H., Sparks, L., Solis-Mezarino, V., Rinner, O., Bork, P. et al. (2013) Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines. Mol. Syst. Biol., 9, 648.
12. Wang, Y., Yang, F., Gritsenko, M. A., Wang, Y., Clauss, T., Liu, T., Shen, Y., Monroe, M. E., Lopez-Ferrer, D., Reno, T. et al. (2011) Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells. Proteomics, 11, 2019-2026.
13. Wis̈niewski, J. R., Zougman, A. and Mann, M. (2009) Combination of FASP and stagetip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. J. Proteome Res., 8, 5674-5678.
14. Cox, J. and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p. p. b.-range mass accuracies and proteome-wide protein quantification. Nat. Biotechnol., 26, 1367-1372.
15. Powell, S., Szklarczyk, D., Trachana, K., Roth, A., Kuhn, M., Muller, J., Arnold, R., Rattei, T., Letunic, I., Doerks, T. et al. (2012) eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res., 40, D284-D289.
16. Nawrocki, E. P., Kolbe, D. L. and Eddy, S. R. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
17. Burge, S. W., Daub, J., Eberhardt, R., Tate, J., Barquist, L., Nawrocki, E. P., Eddy, S. R., Gardner, P. P. and Bateman, A. (2013) Rfam 11.0:10 years of RNA families. Nucleic Acids Res., 41, D226-D232.
18. Zerbino, D. R. and Birney, E. (2008) Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res., 18, 821-829.
19. Rice, P., Longden, I. and Bleasby, A. (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet., 16, 276-277.
20. Götz, S., García-Gómez, J. M., Terol, J., Williams, T. D., Nagaraj, S. H., Nueda, M. J., Robles, M., Talón, M., Dopazo, J. and Conesa, A. (2008) High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res., 36, 3420-3435.
21. de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C. and Mann, M. (2008) Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast. Nature, 455, 1251-1254.
22. Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J. and Aebersold, R. (2011) The quantitative proteome of a human cell line. Mol. Syst. Biol., 7, 549.
23. Geiger, T., Wehner, A., Schaab, C., Cox, J. and Mann, M. (2012) Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins. Mol. Cell. Proteomics, 11, doi:10.1074/mcp. M111.014050.
24. Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W. and Selbach, M. (2011) Global quantification of mammalian gene expression control. Nature, 473, 337-342.
25. Novikova, O., Fet, V. and Blinov, A. (2009) Non-LTR retrotransposons in fungi. Funct. Integr. Genomics, 9, 27-42.
26. Schönknecht, G., Chen, W.-H., Ternes, C. M., Barbier, G. G., Shrestha, R. P., Stanke, M., Bräutigam, A., Baker, B. J., Banfield, J. F., Garavito, R. M. et al. (2013) Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science, 339, 1207-1210.
27. Berka, R. M., Grigoriev, I. V., Otillar, R., Salamov, A., Grimwood, J., Reid, I., Ishmael, N., John, T., Darmond, C., Moisan, M.-C. et al. (2011) Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat. Biotechnol., 29, 922-927.
28. Medina, I., Salavert, F., Sanchez, R., de Maria, A., Alonso, R., Escobar, P., Bleda, M. and Dopazo, J. (2013) Genome Maps, a new generation genome browser. Nucleic Acids Res., 41, W41-W46.
29. Omasits, U., H Ahrens, C., Müller, S. and Wollscheid, B. (2013) Protter: interactive protein feature visualization and integration with experimental proteomic data. Bioinformatics, 30, 884-886.
30. Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature, 425, 737-741.
31. Jensen, L. J., Julien, P., Kuhn, M., von Mering, C., Muller, J., Doerks, T. and Bork, P. (2007) eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res., 36, D250-D254.
32. van Noort, V., Bradatsch, B., Arumugam, M., Amlacher, S., Bange, G., Creevey, C., Falk, S., Mende, D. R., Sinning, I., Hurt, E. et al. (2013) Consistent mutational paths predict eukaryotic thermostability. BMC Evol. Biol., 13, 7.
33. Holder, T., Basquin, C., Ebert, J., Randel, N., Jollivet, D., Conti, E., Jékely, G. and Bono, F. (2013) Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability. Biol. Direct, 8, 2.
34. Sprott, G. D. (1992) Structures of archaebacterial membrane lipids. J. Bioenerg. Biomembr., 24, 555-566.
35. Santos, H. and da Costa, M. S. (2002) Compatible solutes of organisms that live in hot saline environments. Environ. Microbiol., 4, 501-509.