The Hyphal Tip: Fungal Genomes and Comparative Genomics

Webb, C.J., Zakian, V.A. (2008). Identification and characterization of the Schizosaccharomyces pombe TER1 telomerase RNA. Nature Structural & Molecular Biology, 15(1), 34-42. DOI: 10.1038/nsmb1354

Leonardi, J., Box, J.A., Bunch, J.T., Baumann, P. (2008). TER1, the RNA subunit of fission yeast telomerase. Nature Structural & Molecular Biology, 15(1), 26-33. DOI: 10.1038/nsmb1343

Two papers in Nature Structural & Molecular Biology identify the telomerase RNA in Schizosaccharomyces pombe. Telomerase is a multi-unit enzyme that has both protein and RNA components. While the protein subunit is highly conserved and identifiable through sequence comparisons of eukaryotes, the RNA subunit has a variable size and sequence making identification through comparative means more difficult. The S. pombe telomerase RNA subunit, or TER1, was discovered by two labs applying similar biochemical approaches to identify the locus.

WrightFisher talks about a paper & the commentary in Science describing how alignment uncertainty should be taken into account when doing phylogenetic analyses on genomic datastets (some might call this phylogenomics, but Dr Eisen won't). If the sequence alignment is treated as a random variable (and in bayesian approaches have a prior based on result(s) from an alignment program) then more accurate reconstruction. Robin points out

Hyphoid Logic rips on the Alameda Sun for calling Coccidoidies a virus

Hear the BBC radio program on  Fungi: The Fifth Kingdom

On the cover of this week's Nature is a picture of Phycomyces blakesleeanus highlighting the discovery of the MAT locus in this Zygomycete fungus from Alex Idnurm and Joe Heitman and colleagues. While it was previously known that Zygomycetes (the Orange lineage represented by R. oryzae in the tree below) mate, the specific locus has until now, never been discovered. The authors in this study identified the MAT locus through a sequence search looking for HMG-box genes knowing that these are found the Mating Type locus in Basidiomycetes and Ascomycetes. They confirmed the identity through a through set of experiments that included PCR, sequencing and crosses of (+) and (-) strains of P. blakesleeanus, and Southern blots.

A study shows how Caffeine regulates alternative splicing in a subset cancer-associated genes including the transcription factor and tumor suppressor KLF6 through the splicing factor SC35.  There is a necessary "caffeine response element" in the intron of KLF6 which plays a role in the splice-site choice, although caffeine induces up-regulation of SC35 and over-expression of SC35 is sufficient to mimic the caffeine response