Defining “gene”

Blogging about Peer-Reviewed ResearchThe term “gene” might be tired and perhaps because it can have many different meanings – (don’t get us started on homolog!). We of course know that one gene/one enzyme hypothesis and the central dogma fails to represent full complexity of the RNA world, pre- and post-transcriptional gene regulation, and post-transcriptional modifications. An article in PLoS One “Beyond the Gene” from Evelyn Fox Keller and David Harel tackles the perhaps overly stretched definition of the gene.

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Stagonospora nodorum genome published

Blogging about Peer-Reviewed ResearchThe Stagonospra nodorum (teleomorph Phaeosphaeria nodorum) genome is now published in Plant Cell, “Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum”. The paper describes the sequencing and analysis of this Dothideomycete fungus. The analyses included identifying genes likely involved in pathogenecity such as PKS and NRPS genes and enabled the discovery of new genes like ToxA.

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Saccharomyces strain sequencing

Blogging on Peer-Reviewed ResearchWhile many strains of S. cerevisiae are being sequenced, a single strain, YJM789, isolated from the lung of an AIDS patient was sequenced a few years ago at Stanford and published this summer. The genome was described in a paper entitled “Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789”.

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This fungus will trap you (if you are a Nematode)

Blogging about Peer-Reviewed ResearchFungi, like most organisms, take an active role in finding food for survival. When thinking about hostile takeovers by fungi, one probably thinks about mycelia growing towards nutrients, rotting plant matter, the ability to extract nutrients from a living host, or perhaps producing toxins or secondary metabolites that can affect the host. However, some fungi can take an even more active role and trap their animal hosts (when that animal isn’t much bigger than you). A paper from earlier this year on “Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences” describes the evolutionary history of a group of fungi able to trap and eat nematodes. Nematode trapping fungi have been investigated experimentally since at least the 30s (Drechsler, Mycologia. 1937, Drechsler, J Wash Acad Sci. 1933), and some more recent studies of the relationship of the groups (Rubner, Studies in Mycology. 1996).

In the recent PNAS paper, the authors used multi-locus sequencing to reconstruct a phylogeny and history of large group of carnivorous fungi and reconstruct the ancestral history the prey trapping mechanism of either through constricting rings or adhesive traps. They were able to reconstruct the likely order of the evolutionary steps needed to make the stalk and trapping cells. They found that the most common type of trap, an Adhesive Network, was the earliest evolved trap.

Some movies also demonstrate how these fungi make their living.

Amanita toxin genes

A. bisporigeraMichigan State researchers Heather Hallen and Jonathan Walton have reportedly cloned genes from Amanita for alpha-amanitin (mispelled as alpha-aminitin in NYTimes article) which inhibits RNA polymerase II and phallacidin which inhibits actin filament polymerization. The gene sequences are in GenBank for those itching to look at evolutionary relationships of these genes in other fungi.

This is unfortunately another annoying example of science-by-press release where the PNAS publication is not available but the press release and NYtimes article are, but that shouldn’t take aware from a cool result. We also had to wait a week after the dandruff genome announcement to read that paper, I hope the PNAS press-release publication-release timeline gets synchronized soon…

Update: Gene family encoding the major toxins of lethal Amanita mushrooms manuscript is available now.

A writeup about the A. bisporigera “destroying angel” shown here can be read at the Cornell Mushroom blog and the deadly consequences of ingesting it.

[Thanks ShannonS via FredS]


Robin reviews recent Nature paper by Ilan Wapinski et al describing the orthogroups they built from multiple fungal genomes. I’ve been remiss in reviewing the paper myself, but they’ve created an important resource in the SYNERGY tool for orthology identification and a database of orthologs of some ascomycete fungi. I am excited there is a level of interest in the properties of gene duplication and how this may be an important aspect of adaptation and evolution. corn smut

The Cornell Mushroom blog has a nice treatment of the maize pathogen and Mexican delicacy Ustilago maydis corn smut.

Chris and Tom took some more Coprinus pictures while I was away from the lab.