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

The thermophilic fungus Chaetomium thermophilum holds great promise for structural biology. To increase the efficiency of its biochemical and structural characterization and to explore its thermophilic properties beyond those of individual proteins, we obtained transcriptomics and proteomics data, and integrated them with computational annotation methods and a multitude of biochemical experiments conducted by the structural biology community. We considerably improved the genome annotation of Chaetomium thermophilum and characterized the transcripts and expression of thousands of genes. We furthermore show that the composition and structure of the expressed proteome of Chaetomium thermophilum is similar to its mesophilic relatives. Data were deposited in a publicly available repository and provide a rich source to the structural biology community.

[1]  E. Birney,et al.  Velvet: algorithms for de novo short read assembly using de Bruijn graphs. , 2008, Genome research.

[2]  J. Ellenberg,et al.  The quantitative proteome of a human cell line , 2011, Molecular systems biology.

[3]  M. Selbach,et al.  Global quantification of mammalian gene expression control , 2011, Nature.

[4]  M. Mann,et al.  Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast , 2008, Nature.

[5]  Audrone Lapinaite,et al.  The structure of the box C/D enzyme reveals regulation of RNA methylation , 2013, Nature.

[6]  E. O’Shea,et al.  Global analysis of protein expression in yeast , 2003, Nature.

[7]  P. Rouzé,et al.  Current methods of gene prediction, their strengths and weaknesses. , 2002, Nucleic acids research.

[8]  Marta Bleda,et al.  Genome Maps, a new generation genome browser , 2013, Nucleic Acids Res..

[9]  Christian von Mering,et al.  eggNOG: automated construction and annotation of orthologous groups of genes , 2007, Nucleic Acids Res..

[10]  P. Bork,et al.  Consistent mutational paths predict eukaryotic thermostability , 2013, BMC Evolutionary Biology.

[11]  Sean R. Eddy,et al.  Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..

[12]  P. Bork,et al.  Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines , 2013, Molecular systems biology.

[13]  Sean R. Eddy,et al.  Infernal 1.0: inference of RNA alignments , 2009, Bioinform..

[14]  M. Perutz,et al.  Stereochemical basis of heat stability in bacterial ferredoxins and in haemoglobin A2 , 1975, Nature.

[15]  Matthias Mann,et al.  Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome. , 2009, Journal of proteome research.

[16]  V. Fet,et al.  Non-LTR retrotransposons in fungi , 2009, Functional & Integrative Genomics.

[17]  Peer Bork,et al.  Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile , 2011, Cell.

[18]  M. Mann,et al.  Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins* , 2012, Molecular & Cellular Proteomics.

[19]  Justin Powlowski,et al.  Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris , 2011, Nature Biotechnology.

[20]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[21]  M. Beck,et al.  Protein interfaces of the conserved Nup84 complex from Chaetomium thermophilum shown by crosslinking mass spectrometry and electron microscopy. , 2013, Structure.

[22]  Christian H. Ahrens,et al.  Protter: interactive protein feature visualization and integration with experimental proteomic data , 2014, Bioinform..

[23]  G. Sprott.  Structures of archaebacterial membrane lipids , 1992, Journal of bioenergetics and biomembranes.

[24]  J. Banfield,et al.  Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote , 2013, Science.

[25]  Stephan Wickles,et al.  Structural characterization of a eukaryotic chaperone—the ribosome-associated complex , 2012, Nature Structural &Molecular Biology.

[26]  M. Mann,et al.  MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.

[27]  Damian Szklarczyk,et al.  eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges , 2011, Nucleic Acids Res..

[28]  Ronald J. Moore,et al.  Reversed‐phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells , 2011, Proteomics.

[29]  M. Robles,et al.  University of Birmingham High throughput functional annotation and data mining with the Blast2GO suite , 2022 .

[30]  Thomas Holder,et al.  Deep transcriptome-sequencing and proteome analysis of the hydrothermal vent annelid Alvinella pompejana identifies the CvP-bias as a robust measure of eukaryotic thermostability , 2013, Biology Direct.

[31]  I. Longden,et al.  EMBOSS: the European Molecular Biology Open Software Suite. , 2000, Trends in genetics : TIG.

[32]  J. B. Matthew.  Electrostatic effects in proteins. , 1985, Annual review of biophysics and biophysical chemistry.

[33]  H. Santos,et al.  Compatible solutes of organisms that live in hot saline environments. , 2002, Environmental microbiology.

[34]  V. Rybin,et al.  Structural basis of histone H2A–H2B recognition by the essential chaperone FACT , 2013, Nature.