Sometimes choosing a hot lover can make all the difference. In this case, choosing a thermophilic fungus was the right eukaryote for the job to purify stable proteins from the nuclear pore complex and test their interactions. Since high temperatures (60C as compared to what its relative Chaetomium globosum prefers, 24C) will denature proteins, this fungus has evolved the ability to still fold up proteins nicely at those high temperatures. Thus at more standard laboratory room temperature or below, these proteins should be really stable and easier to work with. This manuscript (not OpenAccess sadly) includes the genome sequence of Chaetomium thermophilum sequenced with 454 FLX and XLR at 24X and assembled into 20 scaffolds – (8 chromosomes expected so they say – and I agree – this is quite good).The used the Celera assembler to make this final assembly for those of you taking notes at home on how to assemble your fungal genomes. The genome is available for download at the authors’s site or at GenBank. Their assembly is quite a bit smaller (28.3 Mb) than the related C. globosum (34.9) or Neurospora crassa genome (41Mb – though the authors use the old version and report 39.2; they also say “*based on the published genome (Galagan et al., 2003), although there is a newer assembly of N. crassa available from Broad, the newer assembly is not annotated for protein coding genes yet.” which is kind of weird because there is an annotated version here). I do wonder if the tendency of repeated elements to be collapsed in the assembly process resulted in a smaller assembly or if this really does have a smaller genome and less genes (~7k genes while Neurospora has ~10k). Also worth noting that several other thermophilic fungi have been public for a while at the JGI too – Thielavia terrestris and Sporotrichum thermophile and our lab and others are investigating the genome content and how some genome properties like transposons have evolved in these lineages.
The thermophilic adaptation of this fungus has lead to stable proteins which can be studied more easily than mesophilic fungi. They have been able to determine how the nucleoporins (Nups) interact because of the biochemical and structural assays that are possible with the more stable protein complexes. This highlights the value of targeting an experimental system that has the properties needed and the simple and straightforward tactics needed to generate and use the genome sequence (the genome is but a minor note in the findings of this paper). I can only wonder why none of my de novo genome assemblies go together as nicely as this one, but I’m excited to see this work present new insights into the biology of nuclear pore complexes.
Amlacher, S., Sarges, P., Flemming, D., van Noort, V., Kunze, R., Devos, D., Arumugam, M., Bork, P., & Hurt, E. (2011). Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile Cell, 146 (2), 277-289 DOI: 10.1016/j.cell.2011.06.039