The Hyphal Tip: Fungal Genomes and Comparative Genomics

The 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. I find that often the definition depends on what you want to do with the end product. As the article points out, in bioinformatics this is often about describing regions of sequence so the Sequence Ontology description suffices.

"A gene is: ‘a locatable region of genomic sequence, corresponding to a unit of inheritance, which is associated with regulatory regions, transcribed regions and/or other functional sequence regions’.”

In more general genetics terms this is about inherited material so the authors quote Susan Lindquist describing genetics as "genetics is about the inheritance of traits" rather than solely about the DNA material. This quote is from her research summary and is in the context of prions which provide a mechanism for inheritance outside of nucleic acids. The article does a very nice job taking the reader through some of the different ideas around genes and highlights why protein-coding region alone is not sufficient to define a gene given miRNAs & ncRNAs, binding sites & regulatory regions, and nuances of epigenetics. They do throw a bone back to bioinformatics and the Sequence Ontology definition saying:

"Yet, as the effort of those bioinformatics researchers indicates, there is a common denominator to many uses of that word, and even if it may seem hopeless to fit into the straight-jacket of the old concept of the gene, we do think that common denominator needs to be respected."

The authors go on to propose new jacket for the concepts. A dene that captures the notion of genetic transmission, bene that describes behavior, and a genitor that links a dene to bene. Clear? I think they've generalizing genotype and phenotype and that interaction into more formal terms, but maybe I'm thinking too classically here. The article describes some examples to help define the terms.

• The whole genome can be considered a dene.
• The polypeptide coding region is also a dene (classic protein coding gene definition).
• In cases of alternative splicing each isoform that produces a protein-coding unit is a dene.
• Even things that affect mutation rate, like SSRs, are considered denes.

I wonder what one classifies the units in the NMD regulation of nonsense-isoforms that play a role in SR gene regulation. Is the NMD pathway a bene? What are the nonsense forms considered? They are produced from the pre-mRNA until the concentration of the SR proteins is low and then the productive splicing occurs. I suppose all the isoforms as considered denes here whether or not they actually become proteins if this is regulated event. For the somewhat dismissive tone towards bioinformatics initially, the authors go on to use terms like "Turing-computable truth-valued functions" and "Church/Turing thesis for biology" so they are attempting to provide formal language to make aspects of "fuzzy" biological concepts computable. Something that the ontology consortiums, with their noted shortcomings, have been doing.

The 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. A couple of surprising findings:

• The genome was found to have both Class 1 and Class 2 Hydrophobin genes. Class 2 are normally restricted to basidiomycetes.
• Secreted proteins were not clustered in the genome
  • There appeared to be more secreted proteins shared with the plant pathogen M. grisea and N. crassa indicating some even though they are equidistant to S. nodorum although this analysis would need more sampled genomes of saprotrophic and biotrophic fungi to really support this hypothesis.

The paper has a few more observations about genome organization and synteny conservation, EST analyses of the fungus during infection, and a potential role for horizontal transfer among fungi to exchange pathogenic genes that make it worth taking a look.

While 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". The authors find a few notable rearrangements and unique genes in this strain as compared to the lab and type strain S288C. They find examples of horizontally transferred genes or potentially genes (like RTM1) which are being exchanged among individuals in the population and just not found in first sequenced strain. There are several other genome architecture observations including numbers of indels and highly polymorphic (and thus different from S288C) ORFs. In general the chromosomes are co-linear but they find some rearrangements. One of the main trains of a human pathogenic fungi, which some people will argue aren't really pathogenic since the host must be severely immunocompromised to infect, is the ability to grow at high or body (37 C) temperatures. Most fungi can't survive at this temperature, but this trait is a necessary condition for fungi like Cryptococcus neoformans, Aspergillus fumigatus, and the pathogenic Candida species like C. albicans to infect and potentially overwhelm a host. Previous work from many of the same authors used a QTL approach to map the high temperature phenotype in a clinical strain Saccharomyces using a new genetic technique called reciprocal-hemizygosity to dissect the QTL. This is only the second actual publication of the genome of another strain of Saccharomyces cerevisiae even though there have been several papers profiling rates of evolution in the lab and wild strains S288C, YJM789, and RM11-1A (Gu 2005, Ronald et al 2006) before the final genome paper was published. I doubt we'll keep seeing papers about a single strain sequenced when there is already a reference strain. Instead papers about clusters of strains or closely related species such nearly complete work in other Saccharomyces strains, Coccidioides and Neurospora will probably be the norm. This paper is available as Open Access through PNAS which I applaud the authors for. However, the paper concludes with a paragraph that starts

"Finally, we made the YJM789 genome a free-to-access resource that marks an initial step toward a more complete set of reference sequences for the S. cerevisiae species"

While I am happy to see the sequence resource freely available now, I guess I've come to expect this with any genome publication. The sequence has been available with some restrictions at least since 2003 before the genome was published in a journal. I am unsure why this needs to be championed in the conclusion, shouldn't it be available as a consequence of how it was funded or am I expecting too much?

"This work was supported by National Institutes of Health Grants HG02052 (to R.W.D.), GM068717 (to R.W.D. and L.M.S.), and HG000205 (to R.W.D. and L.M.S.);"

There is more discussion of the project and its future at the Stanford site.

Fungi, 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.

The JGI have released the genome sequence and annotation of the Mycosphaerella fijiensis fungus an important crop pathogen of bananas. This Dothideomycete fungus is one of several in the clade of important plant pathogens that have been sequenced recently including M. gramicola, a relative that causes wheat-blotch.

Michigan 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. 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.

According to Yahoo News (via GT) , Proctor and Gamble published the genome of the dandruff in PNAS (link not yet available) causing basidiomycete fungus Malassezia globosa. The proteins and genome are available at NCBI. Update: PNAS paper available.

New resource on spacialepidemiology.net has maps of Batrachochytrium dendrobatidis infections worldwide. Demoed at recent conference.