Tag Archives: yeast

Aspergillus comparative transcriptional profiling


Researchers from Technical University of Denmark published some interesting results from comparing expression across the very distinct Aspergillus species.

Kudos also goes to making it Open Access. I am posting a few key figures below the fold because I can! They grew the fungi in bioreactors fermenting glucose or xylose. After calibrating the growth curves they were able to sample the appropriate time points for comparison of gene expression across these three species. They found a set of genes commonly expressed.

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Some links


I’ve been too busy to post much these last few days, but here are a few links to some papers I found interesting in my recent browsing.

Schmitt, I., Partida-Martinez, L.P., Winkler, R., Voigt, K., Einax, E., Dölz, F., Telle, S., Wöstemeyer, J., Hertweck, C. (2008). Evolution of host resistance in a toxin-producing bacterial–fungal alliance. The ISME Journal DOI: 10.1038/ismej.2008.19

LEVASSEUR, A. (2008). FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds. Fungal Genetics and Biology DOI: 10.1016/j.fgb.2008.01.004

Shivaji, S., Bhadra, B., Rao, R.S., Pradhan, S. (2008). Rhodotorula himalayensis sp. nov., a novel psychrophilic yeast isolated from Roopkund Lake of the Himalayan mountain ranges, India. Extremophiles DOI: 10.1007/s00792-008-0144-z

New Saccharomyces resequencing assembly

SGRP LogoDavid Carter at the Sanger Centre emailed a message that new assemblies of Saccharomyces strain resequencing project have been posted including a new three-way alignment of S. bayanusS.paradoxusS.cerevisiae. This updates the Dec 2007 release.

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Yeast resequencing update

Ed Louis at Nottingham sent out an email today outlining plans for publishing analyses of the Saccharomyces Genome Resequencing Project.  They are in process of analyzing the data and ask that people respect their use of the data, but also invite collaborations and companion papers.

“If anyone has done or plans on doing a global analysis with a tight clean result which you think should be included in the overview paper, please contact us [Richard Durbin and Ed Louis; emails available through above links]. The analysis would have to be complete by 14 December and you would have to be willing to have the details transparently displayed on the web pages associated with the project.”

Yes, Ecology can improve Genomics

Blogging on Peer-Reviewed ResearchFew organisms are as well understood at the genetic level as Saccharomyces cerevisiae. Given that there are more yeast geneticists than yeast genes and exemplary resources for the community (largely a result of their size), this comes as no surprise. What is curious is the large number of yeast genes for which we’ve been unable to characterize. Of the ~6000 genes currently identified in the yeast genome, 1253 have no verified function (for the uninclined, this is roughly 21% of the yeast proteome). Egads! If we can’t figure this out in yeast, what hope do we have in non-model organisms?Lourdes Peña-Castillo and Timothy R. Hughes discuss this curious observation and its cause in their report in Genetics.

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Yeast genome: Known knowns, and known unknowns

From Genetics this week a review discusses Why are there still 1000 Uncharacterized Yeast genes? Poor Yeast – so many more genes have no known function, while S. pombe has nearly 100% coverage in functional annotation. I’ll also point out that the 1000 genes refers to protein-coding genes, not ncRNA genes which may mean that there is alot more that is unknown.

I think this sentence from the abstract hits the nail on the head.

Notably,the uncharacterized gene set is highly enriched for genes whose only homologs are in other fungi. Achieving a full catalog of yeast gene functions may require a greater focus on the life of yeast outside the laboratory.

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Fungal tree of life papers

Lots of papers in Mycologia (subscription required) this month of different groups analyzing the fine-scale relationships of many different fungal clades using the loads of sequences that were generated as part of the Fungal Tree of Life project.

Some highlights – there are just too many papers in the issue to cover them all. As usual with more detailed studies of clades with molecular sequences we find that morphologically defined groupings aren’t always truly monophyletic and some species even end up being reclassified. Not that molecular sequence approaches are infallable, but for many fungi the morphological characters are not always stable and can revert (See Hibbet 2004 for a nice treatment of this in mushrooms; subscription required).

  • Meredith Blackwell and others describe the Deep Hypha research coordination network that helped coordinate all the Fungal Tree of Life-rs.
  • John Taylor and Mary Berbee update their previous dating work with new divergence dates for the fungi using as much of the fossil evidence as we have.
  • The early diverging Chytridiomycota, Glomeromycota, and Zygomycota are each described. Tim James and others present updated Chytridiomycota relationships so of which were only briefly introducted in the kingdom-wide analysis paper published last year.
  • There is a nice overview paper of the major Agaricales clades (mushrooms for the non-initiated) from Brandon Matheny as well as as individual treatment of many of the sub-clades like the cantharelloid clade (mmm chanterelles…) .
  • Relationships of the Puccinia clade are also presented – we blogged about the wheat pathogen P. graminis before.
  • A new Saccharomycetales phylogeny is presented by Sung-Oui Suh and others.
  • The validity of the Archiascomycete group is also tested (containing the fission yeast Schizosaccharomyces pombe and the mammalian pathogen Pneumocystis) and they confirm that it is basal to the two sister clades the euascomycete (containing Neurospora) and hemiascomycete (containing Saccharomyces) clades. However it doesn’t appear there are enough sampled species/genes to confirm monophyly of the group. There are/will be soon three genome sequences of Schizosaccharomyces plus one or two Pneumocystis genomes – it will be interesting to see how this story turns out if more species can be identified.

This was a monster effort by a lot of people who it is really nice to see it all have come together in what looks like some really nice papers.

Would a Beetle by another name smell as sweet?

I read this blurb in the New Scientist about a PNAS paper (subscription required for next 6 months) on how hive beetles (Aethina tumida) are able to infest bee hives by throwing off the bees because they are producing isopentyl acetate which is thought to be produced and used by bees to signal an alarm. So the increased levels of the pheromone disorients the bees allowing beetles to continue infecting. European bees appear to be susceptible to this attack while the African bees have apparently evolved to better handle the beetle infestation. I’m not clear if the African bees have a different behavior or if they have different biochemical pathways/receptors to not be fooled by the cheap perfume of the invaders.

Beetles + isopentyl acetate = Unstoppable!

The fungus part here is that the beetles are carrying a hemiascomycete yeast, Kodamaea ohmeri in the Saccharomyces clade (see Suh and Blackwell 2005 for more details), which produces the isopentyl acetate pheromone. So it is a sort of auto-immune hive reaction where the defense mechanism is being short-circuited and harming the host.

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Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

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