Exploring a global regulator of gene expression in Aspergillus

Blogging about Peer-Reviewed ResearchWhen first discovered, the gene LaeA was thought to be a master switch for silencing of several NRPS secondary metabolite gene clusters in Aspergillus. NRPS and PKS are important genes in filamentous fungi as they produce many compounds that likely help fungi compete in the ecological niche mycotoxins (e.g. aflatoxin, gliotoxin), plant hormone (e.g. Gibberellin), and a potential wealth of additional undiscovered activities.

A recent paper from Nancy Keller’s lab entitled Transcriptional Regulation of Chemical Diversity in Aspergillus fumigatus by LaeA has followed up previous studies with whole genome expression profiling of a LaeA knockout strain to explore the breadth of the genome that is regulated by this transcriptional regulator. Continue reading Exploring a global regulator of gene expression in Aspergillus

Genome of Postia placenta

The JGI has released the genome sequence and annotation of the Basidiomycete brown rot Postia placenta. Brown rotters can only break down cellulose but do not degrade lignin that white rotters (like Phanerochaete chrysosporium).

Using total genomic DNA from dikaryotic strain MAD-698, the JGI generated 571,000 reads that assembled into 1243 haplotype scaffolds, with 85 of these scaffolds covering half of the genome sequence.

v.1.0 (September 2006): Postia placenta genome assembly v1.0. The assembly release of whole genome shotgun reads was constructed with the JGI assembler, Jazz, using paired end sequencing reads at a coverage of 7.23X. After trimming for vector and quality, 574,631 reads assembled into 1243 scaffolds totaling 90.9 Mbp.

Since Postia placenta is known to be highly polymorphic with a polymorphism rate in the neighborhood of 3-4%, this particular assembly uses extra stringent parameters that should only assemble sections of the genome that are more than 99% identical.The current draft release, version 1.0, includes a total of 17,173 gene models predicted and functionally annotated using the JGI annotation pipeline.

The genome sequence is a whopping 90 Mb – big for a fungus – but I think this is not just the haploid genome since this was DNA from a dikaryon and only the highly identical haplotypes are assembled together (99% identity). So it means that the haploid genome is not likely to be quite this big. This is much like the Candida albicans diploid assembly. Presumably this means any analysis of gene duplicates needs to have at least two levels of classification to distinguish diploid copy from actual duplicated gene.

While nowhere near the density of sampling of genomes in the Ascomycota, the Basidiomycetes are starting to get their due. Kudos to the JGI for tackling this and the DOE and many of the researchers including Dan Cullen to work to get these genomic resources produced. This genome will be important in work to understand forest ecosystems, process of wood rotting, and maybe even in work to develop better fermentation systems for production of biofuels from cellulose.

Mechanism of riboswitch controlling mRNA splicing

A exciting research paper “Control of alternative RNA splicing and gene expression by eukaryotic riboswitches” published in Nature details the mechanism of how riboswitches work in Neurospora crassa. While riboswitches have been found and studied in bacteria there has not been extensive work showing how they work in fungi. In bacteria the riboswitch acts as the direct interacting sensor that switches gene expression off through a structural change in the RNA and fit in nicely with the RNA world view.

Using N. crassa, the authors show that alternative splicing is directly regulated through the thiamine metabolism genes which contains previously identified riboswitches. As also highlighted in the accompanying commentary this is also an interesting examples of direct RNA regulation of alternative splicing rather than through peptides like SR proteins.

The world’s largest organism

Take a guess: what’s the world’s largest organism? No, it’s not Yao Ming. While the Guiness Book of World Records hasn’t weighed in on this issue, scientists out of Oregon State University say that an Armillaria ostoyae individual residing in Oregon’s Blue Mountains is the largest living organism on the planet. Covering 2,200 acres, this tree killing fungus certainly is big. DNA fingerprinting and vegetative pairing confirm that a single individual spans this great distance. In addition to its great size, the fungus is quite old. By using growth rates to estimate age, this scientists estimate that this humongous fungus may be 8,000 years old.

While root rot, the tree killing phenomenon caused by A. ostoyae, slows the rate of tree harvest in a forest, the park service respects the organism’s vital role in the ecosystem. By clearing out old trees, fresh nutrients are resupplied to the soil and room is made for more resistant trees to grow. Besides, how do you kill something that is 1,600 football fields in size?

Evolution of PEX genes

A nice evolutionary analysis of peroxin genes entitled PEX Genes in Fungal Genomes: Common, Rare, or Redundant in the journal “Traffic” from Kiel et al out of the University of Groningen in The Netherlands. Within a species, the genes in the PEX family are not necessarily phylogenetically related to each other, but instead are all named as to how they were discovered in mutant screens, most of which were done in S. cerevisiae.

Peroxisomes are interesting because they are necessary for some biochemical reactions (fatty acid metabolism). In filamentous fungi there are additionally specialized peroxisomes called Woronin bodies that plug the septal pore that separates individuals cells in a hyphae. These are specific to filamentous fungi so it is interesting to contrast the numbers and types of genes in the PEX family that are present as determined from the genome sequences. To relate this to human biology, the authors suggest that understanding the complex phenotypes of human peroxisome biogenesis disorders (PBD) will be helped through the study of the disruptions of PEX genes in various filamentous fungi. Interestingly, they find that nearly all PEX genes are present in all fungi, yeast and filamentous alike, although there may be additional genes unidentified.

Woronin bodies
Woronin bodies in A. nidulans from Momany et al, Mycologia 2002

Continue reading Evolution of PEX genes

Jurassic Park can now Boast Mushrooms

In his book Jurassic Park, Micheal Crichton imagines the possibility to extracting dinosaur DNA from mosquitos entombed in amber and using the extracts to genetically engineer T-rex and Compies alike.  A recent discovery by an avid amber collector and scientists at Oregon State University may help enrich this park of the future: they found a 9 nine-hundredths-inch-long mushroom cap encased in a 100 million year piece of amber (yep, same age as some dinosaur fossils, conveniently enough).

To the avid mycologist out there, this should be the oldest known mushroom and will likely help our understanding of fungal evolution by providing another fossil for phylogeneticists to work with.  Want to read more about the mushroom and the discovery of a tripartite association of the shroom with ancient insects? Check out the Oregonian, then.