Proteins Evolve Differentially in Saccharomyces

Blogging about Peer-Reviewed ResearchPerhaps not a surprise to anyone that has dabbled in evolutionary analysis of proteins, Kawahara and Imanishi (BMC Evolutionary Biology 2007) confirm that not every protein evolves via a molecular clock in Saccharomyces sensu scricto. Using everyone’s favorite evolutionary tool, PAML, the authors identify protein lineages via a whole genome scan that evolve relatively slow or fast compared to the rest of the clade. Some changes even appear to be due to the invisible hand of natural selection and independent of the complications that may have arisen during the whole genome duplication in the ancestor of this clade.

It has been previously speculated that, either upon protein duplication or change in the selective regime of the environment, a protein may rapidly evolve at speciation and then, upon obtaining a new, important function, slow down it’s evolutionary rate to a clock-like tempo. One of the black boxes in this hypothesis is whether or not closely related proteins can rapidly diverge. While the authors are not able to identify a mechanism explaining how, their study demonstrates the plausibility of this hypothesis. However, it remains uncertain if proteins that exhibit rapid divergence will subsequently slow down their evolutionary rate later in time.

It’s good to see evolutionary analysis being applied to fungal genomes. With so many sequenced species spanning a great range of phylogenetic distance, the fungal kingdom is poised to provide great insight into the evolution of eukaryotes.

Fungal Genetics 2007 details

I’m including a recapping as many of the talks as I remember. There were 6 concurrent sessions each afternoon so you have to miss a lot of talks. The conference was bursting at the seams as it was- at least 140 people had to be turned away beyond the 750 who attended.

If there was any theme in the conference it was “Hey we are all using these genome sequences we’ve been talking about getting”. I only found the overview talks that solely describe the genome solely a little dry as compared to those more focused on particular questions. I guess my genome palate is becoming refined.

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Fungal Genetics 2007 summary

A Fungal Genetics 2007 summary.
Wow. What a meeting! I am still exhausted and not just because of the very late Saturday night dancing at the close of the conference. I will just say anyone who thinks scientists are boring people should witness the passion researchers have for their science and in sharing it with other people. Not to mention that some know how to put on their dancing shoes and let loose. Because of the atmosphere at the Asilomar conference center, it really did feel like I was at a super fun science camp that culminated with a rock band and dancing in the big hall.

I am also digesting the science from the talks and social interactions with a variety of people enthusiastic about mycology, genomes, and evolution (which could be a conference unto itsself). There were presentations on a lot of really great topics, from symbiosis between mycorhizal fungi and plants (Laccaria bicolor) to cell wall structure in Cryptococcus. I got to meet so many people who are making an impact in the fungal community both in their research and in the resources provide online. I will try and re-cap so I can remember everything I saw.

Continue reading Fungal Genetics 2007 summary

Hello, do I know you?

Blogging about Peer-Reviewed ResearchSelf and non-self recognition is important for fungi when hyphae interact fuse if they should compartmentalize and undergo apoptosis to kill the heterokaryoton or exchange nutrients. This process is part of cell defense and to limit to the movement of mycoviruses.

A paper in PLOS ONE describes the Genesis of Fungal Non-Self Repertoire. This kind of work goes on down the hall from us as well in the Glass lab among others. This recent paper describes het genes, which contain WD40 repeats and different combinations of these help control specificity. There is of course a diverse literature on this subject especially in Neurospora, and I’m not reviewing it here, but it is an imporant process in understanding how fungi interact with their environment.

Genome resources for Candida species

The Candida clade of Hemiascomycete fungi have received much attention from funding bodies so that many genomic and experimental resources are available address questions of pathogenecity and industrial applications of these species.

The Candida genus

Traditionally, species of yeasts that were thought to be asexual were given the genus name Candida. This has lead to Candida being a sort of taxonomic rubbish bin as this system of classification breaks down when asexuality arises more than once (creating homoplasy). For example, the asexual Candida glabrata is found within the Saccharomyces clade when molecular phylogenetics is applied. The problem lies in that many of these species appear very similar visually and microscopically and so there had not been enough phylogenetically informative phenotypic characters to easily classify them further. With the use of molecular phylogenetics the classifications have been improved as shown in several studies, however we retain the historical nature of the genus and species names for these organisms for the time being even though the phylogenetic diversity of species in the “genus” is much broader than other genus-level classifications. It will be interesting to see whether taxonomic proposals like PhyloCode or traditional revisions of the species names will provide new names for the group.

The Candida Genome Database (CGD) sister to the Saccharomyces Genome Database (SGD) provides resources for phenotype and sequences related to human commensal and dimorphic fungus Candida albicans. A recent paper by Arnaud et al describes the resources that are available through their website. An essentially completed C. albicans diploid genome with curated gene models and annotations provides an essential resource for this model pathogenic system. In addition to the SC5314 strain of C. albicans the white-opaque (WO) strain can switch between different colony morphologies – white and smooth or gray and rod shaped.

6 additional species have had their genomes in the Candida clade have had their genomes sequenced including Pichia stipis, Debaryomyces hansenii, Candida lusitaniae, Candida tropicalis, Candida guilliermondii, and Lodderomyces elongisporus. These resources will hopefully shed some light on the importance and mechanisms for dimorphic switching in the pathogen C. albicans, the importance and evolution of alternative codon usage in the clade, and better usage of the industrial yeasts like P. stipitis and D. hansenii.

Yeast keeps to itself

Cliff Zeyl and Sally Otto present a nice review on research from the Kruglyak lab regarding evidence that Saccharomyces is primarily a selfer in nature as it outbreeds very infrequently (once in 50,000 generations). The implications of this work has relevance on the importance of sexual reproduction and recombination in natural populations.