Location of Repository

Consistent mutational paths predict eukaryotic thermostability

By Vera van Noort, Bettina Bradatsch, Manimozhiyan Arumugam, Stefan Amlacher, Gert Bange, Christopher James Creevey, Sebastian Falk, Daniel R. Mende, Irmgard Sinning, Ed Hurt and Peer Bork

Abstract

Background Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. Results Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1), we could also characterise the molecular consequences of some of these mutations. Conclusions The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.publishersversionPeer reviewe

Topics: thermophily, comparative genomics, protein engineering, eukaryotes, fungi
Year: 2013
DOI identifier: 10.1186/1471-2148-13-7
OAI identifier: oai:cadair.aber.ac.uk:2160/11746
Journal:

Suggested articles

Preview

Citations

  1. (1983). A: The biology of composting: A review. Waste Manag Res doi
  2. (1980). Awad WM Jr: Stabilization of proteins by guanidination.
  3. Becktel WJ: Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding. doi
  4. (2007). Bork P: Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics doi
  5. (2000). BW: Structure and function of the methionine aminopeptidases. Biochim Biophys Acta doi
  6. (2003). Chessel D: Internal correspondence analysis of codon and aminoacid usage in thermophilic bacteria.
  7. (1994). Circadian clock locus frequency: protein encoded by a single open reading frame defines period length and temperature compensation. doi
  8. Cowtan K: Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 2004, 60(Pt 12 Pt 1):2126–2132. doi
  9. (2012). DC: Directed evolution and structural prediction of cellobiohydrolase II from the thermophilic fungus Chaetomium thermophilum. Appl Microbiol Biotechnol doi
  10. (2008). DC: Purification and characterization of a thermostable MnSOD from the thermophilic fungus Chaetomium thermophilum. Mycologia doi
  11. (2002). DG: Multiple sequence alignment using ClustalW and ClustalX. Curr Protoc Bioinformatics doi
  12. (2002). E: 60S pre-ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm. doi
  13. (2007). EI: Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol doi
  14. (1993). Eijsink VG: Stabilization of Bacillus stearothermophilus neutral protease by introduction of prolines. doi
  15. (1997). EJ: Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr doi
  16. (2004). GA: Genomic and proteomic adaptations to growth at high temperature. Genome Biol
  17. (2011). Garcia-Pichel F: Microbial ultraviolet sunscreens. Nat Rev Microbiol doi
  18. (1967). Hudson HJ: The fungi of wheat straw compost: I. Ecological studies. Trans Br Mycol Soc
  19. (2011). Hurt E: Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell doi
  20. (1971). Isolation of thermophilic fungi from self-heated, industrial wood chip piles. Mycologia doi
  21. (1973). JT: Thermophilic fungi in a municipal waste compost system. Mycologia doi
  22. (2009). Kristjansson MM: Effect of proline substitutions on stability and kinetic properties of a cold adapted subtilase. doi
  23. (1990). Lipman DJ: Basic local alignment search tool. doi
  24. (2010). Lo Leggio L: Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family. Biochemistry doi
  25. (2000). Localization and light-dependent phosphorylation of white collar 1 and 2, the two central components of blue light signaling in Neurospora crassa. doi
  26. (2003). LR: The pressure dependence of hydrophobic interactions is consistent with the observed pressure denaturation of proteins. doi
  27. (1975). Microbiological aspects of wood chip storage in tropical environments.
  28. (2004). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res doi
  29. (2001). Ouzounis CA: Identification of thermophilic species by the amino acid compositions deduced from their genomes. Nucleic Acids Res doi
  30. P: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, 38(Database issue):D190–195. doi
  31. (2007). P: Production in trichoderma reesei of three xylanases from Chaetomium thermophilum: a recombinant thermoxylanase for biobleaching of kraft pulp. Appl Microbiol Biotechnol doi
  32. (1989). Phylip - phylogeny inference package (version 3.2). Cladistics doi
  33. (2001). Pushing the boundaries of molecular replacement with maximum likelihood. doi
  34. (2009). Rajoka MI: Optimized expression of a thermostable xylanase 11 a gene from doi
  35. (2000). Ramakrishnan V: Structure of the 30S ribosomal subunit. Nature doi
  36. (2006). RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics doi
  37. (1991). RL: Large differences in the helix propensities of alanine and glycine. Nature doi
  38. (2003). S: Structure of two fungal beta-1,4-galactanases: searching for the basis for temperature and pH optimum. Protein Sci doi
  39. (2000). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol doi
  40. (2009). Sinning I: Structural insights into tail-anchored protein binding and membrane insertion by Get3. Proc Natl Acad Sci USA doi
  41. (2007). Sinning I: The crystal structure of Ebp1 reveals a methionine aminopeptidase fold as binding platform for multiple interactions. FEBS Lett doi
  42. (2010). Sinning I: The structure of Get4 reveals an alpha-solenoid fold adapted for multiple interactions in tail-anchored protein biogenesis. FEBS Lett doi
  43. (2010). Temperature adaptation at homologous sites in proteins from nine thermophile-mesophile species pairs. Genome Biol Evol doi
  44. (2012). Thermophilic fungi in an aridland ecosystem. Mycologia doi
  45. (2003). Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability. doi
  46. (2006). Toward automatic reconstruction of a highly resolved tree of life. Science
  47. (2011). Tsang A: Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris. Nat Biotechnol doi
  48. (2003). Ultrastructural alterations produced by sertaconazole on several opportunistic pathogenic fungi. J Med Vet Mycol 1995, 33(6):395–401. van Noort et al. BMC Evolutionary Biology 2013, 13:7 Page 13 of 13 http://www.biomedcentral.com/1471-2148/13/712. Galagan

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.