TotM: Penicillium vanillyl vaoA and the smell of old literature

old_booksTempus fugit... carpe diem, memento mori... ash to ashes, dust to dust. With such ominous words we express our biggest course, the knowledge of our inevitable demise, for we are sure that time makes no exceptions. The notion of the eroding effects of time in all facets of human experience has baffled us for as long we can remember and is deeply ingrained in our cultural psyche. Every man or woman will die, no matter how powerful they were in life. Every building will eventually crumble, no matter how majestic. Every word that has been said will ultimately be forgotten, no matter the deep impact they may have in our word. With the advent of modern times, we discovered that poetry was right. We are doomed by thermodynamics to an endless entropic abyss and that same fate defines time itself.  With such ominous fate awaiting, humanity tried to fight back. In order to make our thoughts transcend time and achieve eternity we invented writing, as a form to preserve in time our most ethereal legacy.



But even then, even Shakespeare will be forgotten one day. The symbols are still written in matter, and matter is subjected to the same unbreakable laws as our bodies. Compare a new book and one that’s decades old and you’ll observe how the paper itself gets yellow, frailer than yesterday but stronger than tomorrow. Paper, as we all know, is made of wood. It is by no means a formidable material, made of a combination of organic polymers: cellulose, lignocellulose and lignin, mostly. Lignin in particular, is an extremely diverse family of chemicals made of arrays of aromatic subunits. Such complexity makes wood extremely resilient to microbial attacks, to the point that only certain fungi in the Agaricomycotina clade are able to fully digest it. With time, however these compounds start to break by action of oxygen, releasing chemicals that damage the structure and produce the characteristic smell of old literature.

 799px-Vanillyl-alcohol_oxidase_reaction.PNGWhile the ability to digest lignin is very uncommon in nature, eating plant matter is quite the opposite. Those critters must find ways to avoid the toxic effects of lignin-derived chemicals, and that imply a big pool of detoxifying enzymes. The vanillyl alcohol oxidase (VAO) superfamily contains a myriad of flavoproteins, many of which are involved in the degradation of organic compounds derived from lignin. It includes, naturally, vanillyl alcohol oxidase itself (vaoA), an enzyme first characterized in Penicillium. As we can observe in our tree of the month from the Penicillium digitatum phylome, the evolutionary story of this protein family is quite dynamic, as expected given the nature of the compounds they are meant to eliminate.





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