Wednesday, June 27, 2012

Mushroom seen in USA Today!

'Magic' Mushroom G. lucidum
Credit: Wikipedia user Eric Steinert
While peering through the evening's Twitter foliage, I spotted a fungal gem among the fallen, matted links of my "social media ecosystem." Following the trail blazed by Matt Herper and Shrikant Manti, I hiked over to USA Today's ScienceFair blog to read "Chinese 'mushroom of immortality' genome mapped," by Dan Vergano. Great title, but what about the post itself?

Vergano explores the recently-reported genome of the lingzhi / reishi mushroom (G. lucidum), an Asian traditional medicine with a rich pharmacopoeia. The reader gets a brief summary, slightly sparse and unstructured - note the oft-used hook "the study authors note," a sure sign that we're venturing into uneasy territory - and a few throwaway terms, like "Triterpenoids" [sic] and "more than 12,600 genes" (that's a mighty round number for any organism, I'd say...). The piece feels strangely unfinished, like it lost all its momentum after the initial burst from a catchy headline.

Laccase 'lights up' lignins!
Source: Mashed-up from Zeeco and U-Maine
So, it's off to Nature Communications for a more thorough look at the item of interest. Sure enough, looks like the bulk of the USA Today post simply paraphrases the opening paragraph of the manuscript! From mentioning "400 compounds" to a passing remark about biofuel production, it's all there. But where did the strange '12,600' value come from? We'll turn things over to lead authors Chen, Xu, and Liu: Table 1 states that the G. lucidum genome contains 16,113 protein-coding genes, and further down (Fig. 2b), a Venn diagram shows that 12,646 genes are expressed throughout the fungus' life cycle. Now we're getting somewhere! The authors go on to discuss bioactive polysaccharides, mysteriously absent from the post, and then the variety of -ases that contribute to the 'enzymatic combustion' of wood lignins...the best quotes are always buried!

He knows fungal gene mapping
Source: KT5 blog
Instead of heaping on further criticism, let's fill in some blanks here. Triterpenoids aren't so much individual compounds as a family affair - the catch-all term refers to any compound produced by stitching together six isoprenes, a small 5-carbon synthon common to all plant life. Perhaps you've seen lots of triterpenoids without recognizing them: lanosterol, the precursor to human sex hormones testosterone and estrogen, falls into this class. If you're more chemical biology-inclined, check out the Discussion, where the authors use gene sequence and mapping technologies - SMURF, anyone? - to predict zinc-finger nuclease clusters, and then discuss the secondary metabolites arising from a wide variety of expressed cytochrome P450 (CYP) enzymes, the original biochemical bandits behind selective C-H oxidation

(P.S. - This mushroom really represents in the primary literature: a search for the term "lucidum" only brought up 140 hits at ACS, but this ballooned to 2,955 at Wiley, and 5,000+ at ScienceDirect!)

1 comment:

  1. Do you have a recipe in the works? A stir-fry, perhaps?