Tag Archives: Fungi

Horizontal Gene Transfer In Ascomycete Fungi

Horizontal Gene Transfer (HGT) goes against what we typically consider the normal transfer of genetic material from parent to offspring.  HGT involves the transfer of genetic material from one organism to another.  Within the bacteria, whose mode of survival typically depends on phagocytosis, there is a fairly amount of HGT.  Events of HGT have been rarely observed in Eukaryotes because numerous barriers exist to prevent foreign nucleotides from entering a cell’s nucleus.  Some of these barriers in the Fungi include a substantial cell wall made of chitin, multiple cell and nuclear membranes to cross, and the secretion of metabolic enzymes to the outside of the cells and subsequent uptake of the nutrients.  Despite these barriers, there is now evidence of multiple occurrences of HGT in the fungi.

In a recent article published in the journal Current Biology, Jason Slot and Antonis Rokas, both of Vanderbilt University, provided evidence of HGT in two Ascomycete clades.  In this study, the authors identified a 23-gene cluster from the genus Aspergillus which relocated to the genus Podospora.  Genes that are in this cluster synthesize the toxic compound, Sterigmatocystin, which is a precursor to aflatoxins, noted for their production in Aspergillus.  Both genera are located in the subphylum Pezizomycotina, so each clade is not distantly related, but HGT was observed using different methods.

While it’s easy to observe genetic material passed from generation to generation, recognizing HGT is a little more difficult.  The main way the researchers have identified HGT is using phylogenetic methods to identify gene clusters whose homology cannot be explained by lineage alone.

Thomas Richards points out in his commentary on the Slot & Rokas paper (also in Current Biology), that because fungi do not phagotrophically consume their food they are less likely to incur HGT event.  There are two notable hypotheses to why we do see HGT in the fungi.  First, many secondary pathway genes in Eukaryotes are encoded in gene clusters, and the fungi have a fair amount of these clusters.  Gene clusters, which are more functional in a natural selection sense, are therefore more likely to persist upon transmission, as opposed to individual genes.  Data from HGT studies in fungi support this hypothesis.  Second, fungi are naturally, from the basis of their biology and natural history, intimately tied to other organisms, and fulfill roles as saprobes, pathogens, or symbionts.  This close intimacy increases the opportunity for genes to transfer from one organism to another.  Data suggests that this hypothesis is true also, as many of the recorded instances of HGT in fungi have been observed in organisms with overlapping environments.

The International Mycological Association’s Fungus Journal

The International Mycological Association has upgraded their recently inaugurated journal IMA Fungus (see here and here) and joined with the Ingenta Connect group of journal publishing.  I have high hopes for the content of this journal in the future as there is an excellent group of editors and researchers on the steering committee.  Too bad it doesn’t look like it will become open access.

First Steps Toward Learning the Language of Mycorrhizal Communication

I’ve already talked about mycorrhizal associations numerous times (here and here), so if you’re not already used to hearing about mycorrhizae, you will if you continue to read this blog.  In this recent paper, entitled “Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza“, published online in the journal Nature, the authors Maillet et al address plant and fungal interactions of arbuscular mycorrhizal associations.  Using the Glomus intraradicesMedicago truncatula model system, the researchers identify diffusible chemical signals produced by the fungus during initiation of the mycorrhizal association with the plant.

It has been hypothesized that both fungi and bacteria interacting with plant roots do so using similar genetic mechanisms.  It has already been shown that rhizobial bacteria – particularly the nitrogen fixing microbes associated with leguminous plants – produce lipochitooligosaccharide (LCO) signals used in the  communication with host plants.  The authors of this study discovered that the fungus Glomus intraradices, like the nitrogen-fixing bacteria, secretes an array of sulfated and non-sulfated simple LCOs which stimulated the formation of arbuscular mycorrhizae in disparately related plants, such as Medicago (Fabaceae), Daucus carota (Wild Carrot; Apiaceae), and Tagetes patula (French Marigold; Asteraceae).  These compounds were found in Glomus intraradices both interacting with plant roots and in free-living resting spores in the soil.

Comparing the genes involved in the transduction of the LCO signals in both rhizobial bacteria associated with legumes and arbuscular mycorrhizal fungi associated with land plants yielded similar gene expression pathways.  In order to validate the role of LCOs in mycorrhizae formation, the researchers genetically engineered non-plant interacting bacteria to produce the LCOs from Glomus.  These engineered bacteria increased mycorrhizae formation in plants already associated with Glomus.  Fungal LCOs were also found to induce root branching, a trait long associated with the formation of mycorrhizae in plants.  There is a nice commentary on this research article located here.

Lessons Learned from Ectomycorrhizal Fungal Genome Sequencing

Genome sequencing has provided us with an amazing amount of information regarding organismal biology and mycorrhizal fungi are some of the most interesting of the organisms who have had their genomes sequenced.  Maybe I am a little partial to these fungi because I study them intimately, but new sequencing technology has made this an exciting time for people like me.

Ectomycorrhizal fungi are a polyphyletic group of organisms which form a symbiotic association with the roots of tree species (the word ‘mycorrhizal’ literally means plant-fungal unions).  This association has typically been recognized by the exchange of nutrients and water from the fungus to the plant and the exchange of sugars derived from photosynthesis from the plant to the fungus.  Although ectomycorrhizal fungi only form mycorrhizae  with 3% of plant species (arbuscular and other mycorrhizal fungi associate with approximately 92% of plants), these associations are with a diverse array of plant lineages, including the Betulaceae, Cistaceae, Dipterocarpaceae, Fabaceae, Fagaceae, Myrtaceae, Pinaceae, and Saleceae.  Plants in these families cover almost the entire portion of boreal, temperate, Mediterranean, and sub-tropical woodlands, so their importance is significant.  It’s very interesting to note that these associations have independently arisen at least eight times within the angiosperms and between six and eight times in the gymnosperms.  Mycorrhizal associations are thought to have originated when plants and fungi climbed onto land together (more on that here).

The sequencing of both fungal and plant genomes over the last few years has led to greater understanding of how these organisms interact during their mutualistic associations.  Although genome sequencing has addressed some long established questions, there are many more questions that have arisen from these sequencing efforts.  This recent review in Trends in Genetics by Jonathan Plett and Francis Martin of INRA-Nancy, two of my collaborators, addresses the current state of our knowledge of  the ectomycorrhizal symbiosis and poses directions for future research in this vital research area.

Currently, only two ectomycorrhizal fungal genomes (Basidiomycete mushroom Laccaria bicolor & Ascomycete truffle Tuber melanosporum) have been sequenced, but other fungi (see the Mycorrhizal Genomes Project) are scheduled to be sequenced by the Martin Lab through JGI.  With a genome size of 65 Mb Laccaria bicolor has the largest amount of protein coding regions of any sequenced fungus, and Tuber melanosporum has the largest genome of any sequenced fungus at 125 Mb but has one of the least dense genomes.

The nature of mutualistic symbiotic relationships imply that both organisms benefit from the association and both ectomycorrhizal fungi and their host plants fulfill this criteria.  Unlike saprotrophic fungi, ectomycorrhizal fungi are very poorly suited to degrade cellulosic plant material, but they are able to access soil nutrients via a large biological toolbox of secreted proteases and phosphorus transporters.  Both Laccaria bicolor and Tuber melanosporum, which have very different genomes, exhibit a very similar suite of symbiosis-induced nutrient cycling enzymes, which suggest that providing nutrients to the host plant is a key defining feature of ectomycorrhizal fungi.  Interestingly, Laccaria bicolor and Tuber melanosporum rely on differing mechanisms of interacting with their host and acquiring carbon from the environment.  Laccaria bicolor appears to be less dependent on the host and more active at acquiring carbon from the soil substrates and, as a result, may act as a weak saprotroph in the environment.  Tuber melansporum is more aggressive in its colonization of plant roots and does not appear to be able to acquire carbon from the soil and therefore is more dependent on the host for its survival.

Information gathered from fungal genomes suggests that a majority of the biochemical and genetic control over the initiation of the mycorrhizal association comes from the fungal partner, which makes sense given that the fungus has more energy to gain from the association.  Most mycorrhizal fungi are unable to acquire carbon from the environment so they are completely reliant on hand outs from their host plants.  It appears that mutualistic fungi share similar mechanisms with pathogenic fungi and bacteria when interacting with plants, including the use of small secreted proteins which interact directly with plant cells.

With the sheer amount of genomic data being generated it’s an exciting time to be a scientist, especially one who studies mycorrhizal fungi.  Over the next few years, especially with sequencing projects scheduled for completion, we will have even more data to shed light on the amazing biological associations of plants and microbes.

(Above Photo: section of Populus/Laccaria ectomycorrhizal root – JM Plett © INRA)

Bioenergy Trees – An Upcoming New Phytologist Symposium

Fuels derived from cellulosic biomass are increasingly becoming a priority as we focus both on reducing the large amount of greenhouse gases we introduce into the atmosphere and our dependence on unsustainably sourced fossil reserves.  Liquid or solid biofuels derived from cellulosic materials, such as trees, will address these criteria while also assisting agricultural development in rural areas by promoting sustainable coppice harvesting on marginal lands not suitable for consumption crop production.  The use of next-generation genomics technologies, as well as more traditional biological research methods, will help develop and enhance tree growth in no- to low-input environments.  Additionally, genomic resources will contribute to understanding the process of cell wall formation in woody plants and allow researchers to optimize the composition of plant cell walls for bioenergy concerns.

In the upcoming meeting “Bioenergy Trees” – sponsored by the journal The New Phytologist in their ongoing series of symposia – will address the development of trees and other woody biomass for bioenergy purposes.  This meeting will be held at INRA-Nancy, in Nancy/Champenoux, France, from May 17th to 19th, 2011.  Registration is now open.  In addition to this very pertinent research topic, Nancy is truly a magical place, so it’s with great excitement that I tell you about this meeting.

In addition, The New Phytologist has announced the next round of symposia for 2012 here.

Comparative Genomics Of Eukaryotic Microorganisms Meeting

I’m not sure if I am going to be able to make this meeting, but I thought I would pass on the information to you.  The list of speakers is excellent and it’s in a beautiful location.  This is a biannual meeting on the comparative genomics of Eukaryotic microorganisms sponsored by the European Molecular Biology Organization (EMBO).

Registration and meeting information is located here.