Consistent mutational paths predict eukaryotic thermostability

Abstract

BackgroundProteomes 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.ResultsStudying 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.ConclusionsThe 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.

Interaction of the cotranslational Hsp70 Ssb with ribosomal proteins and rRNA depends on its lid domain

“…Therefore, we set out to determine the crystal structure of Ssb from the thermophilic fungus Chaetomium thermophilum 3334, which is 75% identical to Ssb1 from Saccharomyces cerevisiae . Within the Hsp70 family, domain organization is highly conserved (Fig.…”

“…We determined the structure of full-length Ssb from the thermophilic Ascomycota Chaetomium thermophilum 3334 in the open ATP-bound conformation and characterized its ribosome binding by crosslinking and mutagenesis experiments. Ssb is positioned on the ribosome by dual interaction with ribosomal proteins and rRNA in close proximity of the tunnel exit.…”

Interaction network of the ribosome assembly machinery from a eukaryotic thermophile

“…Overall, we could determine the structures of 14 different targets [ Fig. 1(B)] including 12 published (e.g., ctAcl4, ctSyo1, ctArx1, ctSqt1, ctYtm1, ctErb1, ctMrt4, ctRio2, ctCrm1, ctMtr2, ctMex67, and ctRsa4 19,32,[38][39][40][41][42][43][44][45] ) as well as ctTif6, and ctYvh1 [ Fig. 1…”

Proteome evolution of deep-sea hydrothermal vent alvinellid polychaetes supports the ancestry of thermophily and subsequent adaptation to cold in some lineages

“…2012), a marked CvP_bias similar to C. thermophilum (Holder et al. 2013) and, more surprisingly, a strong increase in the number of alanine, a characteristics that is only shared with the thermophilic fungi Thielavias (van Noort et al. 2013).…”