Strep­to­myces At­las

by Me­chas and Roberto

Most of the nat­ural prod­ucts in clin­i­cal use come from Acti­nobac­te­ria. Among the Acti­nobac­te­ria, soil Strep­to­myces species stand out as an in­valu­able source of bioac­tive mol­e­cules, such as an­tibi­otics, an­ti­fun­gals, an­ti­cancer agents, and im­muno­sup­pres­sants. In ad­di­tion to be­ing pro­lific pro­duc­ers of sec­ondary metabo­lites, these mi­crobes also have com­plex reg­u­la­tory sys­tems. 

As in so many ar­eas of bi­ol­ogy, ge­nomics has also be­come cen­tral to the study of Acti­nobac­te­ria. Since the com­ple­tion of the first genome of the model or­gan­ism Strep­to­myces coeli­color some 25 years ago, the num­ber of avail­able genomes and tools to an­a­lyze them has grown im­mensely. But more data also in­tro­duces new and greater chal­lenges. Among these is un­der­stand­ing how these mi­crobes, whose genomes con­tain large ar­rays of genes for nat­ural prod­ucts, reg­u­late and ex­press this in­for­ma­tion to op­ti­mize growth and metabo­lite pro­duc­tion. 

Which is why a new tool for as­sess­ing reg­u­la­tory net­works, Strep­TRN, is such a wel­come ad­di­tion to the field. Thanks to a col­lab­o­ra­tion among Wa­genin­gen Uni­ver­sity, DOE Joint Genome In­sti­tute, Lei­den Uni­ver­sity, and the Uni­ver­sity of Liege, re­searchers gen­er­ated a brows­able at­las of Strep­to­myces and re­lated actin­o­mycetes. The goal is to pro­vide re­searchers with a tool to ex­plore tran­scrip­tional con­trol, from genes to net­works, that may lead to new pre­dic­tions and a deeper un­der­stand­ing of Acti­nobac­te­r­ial bi­ol­ogy and me­tab­o­lism. 

Reg­u­la­tory net­work of tran­scrip­tion fac­tor (TF) cross-reg­u­la­tion. Nodes rep­re­sent TFs; edges in­di­cate TF bind­ing sites (TF­BSs) iden­ti­fied up­stream of other TFs. Node size re­flects the num­ber of TF­BSs (small, medium, large), and or­ange nodes de­note TFs with pre­vi­ously char­ac­ter­ized bind­ing sites. Source

In the words of our close friend and se­nior au­thor Gilles van Wezel: the aim is for "Strep­TRN to serve the com­mu­nity in much the same way as StrepDB: as a brows­able, search­able en­try point for ex­plor­ing Strep­to­myces bi­ol­ogy, in this case fo­cused on reg­u­la­tory net­works."

What is best is that Strep­TRN is a com­mu­nity re­source, open for all to use, that will be con­tin­u­ously up­dated. We urge all those in­ter­ested to ex­plore this mar­velous on­line re­source in their search for an­swers re­gard­ing Acti­nobac­te­ria and, why not, per­haps the next promis­ing nat­ural prod­uct.