A postdoc or research scientist position is available at at University of Arizona and USDA-ARS in the lab of Peter Cotty to work on Aspergillus flavus including constructing a database of whole genome sequences of vegetative compatibility groups. See the position advertisement for more information.
In a letter to the editor to the journal Nature, regarding the recently discovered/induced sexual stage in Aspergillus fumigatus, David Hawksworth argues that using the separate names for sexual (teleomorph) and asexual (anamorph) stages is confusing and unnecessary in this context. The name Neosartorya fumigata is given to the sexual stage which was produced from two individuals which were both A. fumigatus. The letter writer makes the point that referring to a new name for the sexual stage when we already know what its anamorph is seems superfluous and overly confusing. He gives the analogy of Aspergillus nidulans where its teleomorph Emericella nidulans is “largely ignored”.
The double names for something which is the same species (i.e. has the same genomic sequence) is certainly a confusing aspect of mycology. It stems from the morphological description of species and that before DNA or molecular approaches to identification it was difficult to connect the anamorph and teleomorph stages unless you could induce the entire lifecycle in the laboratory. I think that the same name for homologous structures from different phyla is also equally confusing, but necessary aspect of how things are currently named and classified.
What researchers should described the sample/individual they are using for experiments in their manuscripts is important to avoid confusion and for readers so I think Prof Hawksworth makes an important point especially when discussing something where the anamorphs and teleomorphs are unified. Certainly an agreed upon protocol here would be quite helpful of what to preferably use when the stages have been connected.
Hawksworth, D. (2009). Separate name for fungus’s sexual stage may cause confusion Nature, 458 (7234), 29-29 DOI: 10.1038/458029c
Shepard Fairley has gotten alot of notice lately for his Obama art that has been replicated pretty much everywhere. I mocked up a homage to his earlier street art — here we’ll discuss the growing Aspergillus genome posse.
But the work from mainly the JCVI, Broad Institute, JGI, NITE, and Sanger centre has generated an excellent collection of genome sequences for the Eurotiales clade (feel free to get a login for the wiki and add other that are missing). The Aspergillus community now has a AGD – Aspergillus Genome Database project that includes a curator of genome annotation (they are hiring) and presumably literature in the SGD and CGD model of curation.
I think a lot of other projects have a Posse too (or maybe just a loosely organized band) in terms of a community of people working on related species and willing to work together to coordinate. As these sort of “clade” databases start to develop we will have better clusters of information that can be mapped among multiple species.
Eventually I hope this will spur efforts for more coordinated genome databases for comparative genomic and transfer of known gene and functional information between experimental systems. The efforts really require coordination or centralization of the data so that gene models can be updated as well as orthologs and phylogenomic inference of function.
A manuscript at Nature AOP details the success of the Dyer lab and collaborators in encouraging Aspergillus fumigatus to complete the sexual cycle under observable (e.g. laboratory) conditions. The authors are the teleomorph (sexual or perfect) stage Neosartorya fumigata for a fungus that had been previously only had an observed anamorphic stage. A. fumigatus can reproduce asexually forming structures called conidiophores which produce asexual spores called conidiospores (or mitospores as they are produced via mitosis) define the anamorph or imperfect stage, but no sexual structures such as cleistothecia that produce the packaged sexual products as ascospores. See a presentation by David Geiser (archived at the Aspergillus website) for more detail on some of the morphological and phylogenetic characters that unify the group of Eurotiales fungi.
Like several other groups of fungi, A. fumigatus was presumed to have a putative cryptic sexual stages inferred from population genetic evidence of sexual recombination, but until no telemorphs had been observed. In addition, an observed perfect stage doesn’t necessarily indicate it is easy to induce mating in laboratory conditions. Complicated media including the ever stressful V8 juice was needed to induce mating in the basidiomycete yeast Cryptococcus neoformans (Erke, J Bacteriol 1976). In fact, Christina Hull’s lab has shown we still don’t even know what ingredients in V8 juice even induce mating (Kent et al, AEM 2008)! Other fungi including Coccidioides have been implicated as cryptically sexual (Burt et al, PNAS 1996) but no one has been able to induce mating in laboratory conditions. In this case a petri plate with a individual of each mating type (since this is a heterothallic fungus), and a series of different media conditions provided an environment suitable for mating to occur.
The work in this paper follows from their previous work identifying isolates of different mating types (Paoletti, Current Biol, 2005). The discovery of sexual stage for Aspergillus fumigatus (which Brent cannot pronounce) is a boon for molecular geneticists in construction of knockout strains and ability to follow recombination. While A. nidulans is a sexual species and model system for genetics, it is useful to have more tools to directly manipulate A. fumigatus and directly test hypotheses about genes involved in pathogenicity.
This observation of meiosis in the laboratory is also is interesting to considered in light of work that RIP is active in other Aspergillus species (and also see this post) suggesting that RIP may be operating under meiotic conditions.
Isolates of different mating types have also been described for the putatively asexual Coccidioiodes (Mandell et al, EC 2007; Fraser et al, EC 2007) so it remains a possibility that we can also induce sexual recombination in laboratory conditions in this fungus.
Céline M. O’Gorman, Hubert T. Fuller, Paul S. Dyer (2008). Discovery of a sexual cycle in the opportunistic fungal pathogen Aspergillus fumigatus Nature DOI: 10.1038/nature07528
A quick post of some recent comparative genomics papers on our desk that are worth a look.
- Khaldi N, Wolfe KH (2008) Elusive Origins of the Extra Genes in Aspergillus oryzae. PLoS ONE 3(8): e3036. doi:10.1371/journal.pone.0003036. This was a cool but somewhat controversal finding presented at Fungal Genetics last year.
- Casselton, LA. Fungal sex genes – searching for the ancestors. doi: 10.1002/bies.20782. A review of recent findings about the Zygomycete MAT locus.
- Soanes DM, Alam I, Cornell M, Wong HM, Hedeler C, et al. (2008) Comparative Genome Analysis of Filamentous Fungi Reveals Gene Family Expansions Associated with Fungal Pathogenesis. PLoS ONE 3(6): e2300. doi:10.1371/journal.pone.0002300
- Lee DW, Freitag M, Selker EU, Aramayo R (2008) A Cytosine Methyltransferase Homologue Is Essential for Sexual Development in Aspergillus nidulans. PLoS ONE 3(6): e2531. doi:10.1371/journal.pone.0002531
The Trichoderma reesei genome paper was recently published in Nature Biotechnology from Diego Martinez at LANL with collaborators at JGI, LBNL, and others. This fungus was chosen for sequencing because it was found on canvas tents eating the cotton material suggesting it may be a good candidate for degrading cellulose plant material as part of cellulosic ethanol or other biofuels production. The fungus also has starring roles in industrial processes like making stonewashed jeans due to its prodigious cellulase production.
The most surprising findings from the paper include the fact that there are so few members of some of the enzyme families even though this fungus is able to generate enzymes with so much cellulase activity. The authors found that there is not a significantly larger number of glucoside hydrolases which is a collection of carbohydrate degrading enzymes great for making simple sugars out of complex ones. In fact, several plant pathogens compared (Fusarium graminearum and Magnaporthe grisea) and the sake fermenting Aspergillus oryzae all have more members of this family than does. T. reesei has almost the least (36) copies of a cellulose binding domain (CBM) of any of the filamentous ascomycete fungi. They used the CAZyme database (carbohydrate active enzymes) database which has done a fantastic job building up profiles of different enzymes involved in carhohydrate degradation binding, and modifications.
Whether T. reesei is really the best cellulose degrading fungus is definitely an open question. That it works well in the industrial culture that it has been utilized in is important, but there may be other species of fungi with improved cellulase activity and who may in fact have many more copies of cellulases. So it will be good to add other fungi to the mix with quantitative information about degradation to try and glean what are the most important combination of enzymes and activities.
One technical note. The comparison of copy number differences employed in the paper is a simple enough Chi-Squared, work that I’ve done with Matt Hahn and others include a gene family size comparison approach that also taked into account phylogenetic distances and assumes a birth-death process of gene family size change. It would be great to apply the copy number differences through this or other approaches that just evaluate gene trees for these domains to see where the differences are significant and if they can be polarized to a particular branch of the tree.
So will this genome sequence lead to cheaper, better biofuel production? Certainly it provides an important toolkit to start systematically testing individual cellulase enzymes. It’s hard to say how fast this will make an impact, but the work of JBEI and a host of other research groups and biotech companies are going to be able to systematically test out the utility of these individual enzymes.
There is also evolutionary work by other groups on the evolution of these Hypocreales fungi trying to better define when biotrophic and heterotrophic transitions occurred to sample fungi with different lifestyles that might have different cellulase enyzmes that may not have been observed. Defining the relationships of these fungi and when and how many times transitions to lifestyles occurred to choose the most diverse fungi may be an important part of discovering novel enzymes.
Martinez, D., Berka, R.M., Henrissat, B., Saloheimo, M., Arvas, M., Baker, S.E., Chapman, J., Chertkov, O., Coutinho, P.M., Cullen, D., Danchin, E.G., Grigoriev, I.V., Harris, P., Jackson, M., Kubicek, C.P., Han, C.S., Ho, I., Larrondo, L.F., de Leon, A.L., Magnuson, J.K., Merino, S., Misra, M., Nelson, B., Putnam, N., Robbertse, B., Salamov, A.A., Schmoll, M., Terry, A., Thayer, N., Westerholm-Parvinen, A., Schoch, C.L., Yao, J., Barbote, R., Nelson, M.A., Detter, C., Bruce, D., Kuske, C.R., Xie, G., Richardson, P., Rokhsar, D.S., Lucas, S.M., Rubin, E.M., Dunn-Coleman, N., Ward, M., Brettin, T.S. (2008). Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nature Biotechnology DOI: 10.1038/nbt1403
A paper in Science from Jason Crawford and colleagues explores the function of polyketide synthetases (PKS) in the synthesis of the secondary metabolite and carcinogen aflatoxin. Previous work (nicely reviewed in the fungi by Nancy Keller and colleagues) has shown the the PKS genes have several domains. These domains include acyl carrier protein (ACP), transacylase (SAT), ketosynthase (KS), malonyl-CoA:ACP transacylase (MAT), “product template” PT, Aand thioesterase/Claisen cyclase (TE/CLC). These domains make up PksA, but the specific role of each domain’s in synthesis steps has not been fully worked out. Understanding this process and the specificity of the chemical structures that are created can help in redesign of these enzymes for synthesis of new molecules and drugs.
Then authors cloning and combining the domains from a cDNA template of pksA [accession AY371490] (from Aspergillus parasiticus) into various combinations and then evaluated the synthesized products via HPLC. This deconstruction of a complicated protein and its domains is a great example of functionally mapping the role of each part of the enzyme and integrating with the biochemistry of the synthesized products. The findings of this research also mapped a role for the PT product template domain which could suggest where modifications could be made to tweak the synthesized products by these enzymes.
Crawford, J.M., Thomas, P.M., Scheerer, J.R., Vagstad, A.L., Kelleher, N.L., Townsend, C.A. (2008). Deconstruction of Iterative Multidomain Polyketide Synthase Function. Science, 320(5873), 243-246. DOI: 10.1126/science.1154711
A paper in Current Genetics describes the discovery of Repeat Induced Polymorphism (RIP) in two Euriotiales fungi. RIP has been extensively studied in Neurospora crassa and has been identified in other Sordariomycete fungi Magnaporthe, Fusiarium. This is not the first Aspergillus species to have RIP described as it was demonstrated in the biotech workhorse Aspergillus oryzae. However, I think this study is the first to describe RIP in a putatively asexual fungus. The evidence for RIP is only found in transposon sequences in the Aspergillus and Penicillium. A really interesting aspect of this discovery is RIP is thought to only occur during sexual stage, but a sexual state has never been observed for these fungi. Continue reading