Novel function in light-mediated microbial processes

Title Discovering functional novelty in metagenomes: examples from light-mediated processes Running Title (54 chars allowed) Novel function in light-mediated microbial processes Abstract 1 The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of 2 discovering functional novelty using computational tools. Here, we apply three different 3 concepts for predicting novel functions within light-mediated microbial pathways in five diverse 4 environments. Using phylogenetic approaches, we discovered two novel deep-branching 5 subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV 6 environments. Using neighborhood approaches, we were able to assign to BLUF domain-7 containing proteins (involved in light-sensing) seven novel functional partners in luciferase 8 synthesis, nitrogen metabolism, and quorum sensing. Finally, by domain analysis, we predict for 9 RcaE proteins (involved in chromatic adaptation) sixteen novel domain architectures that 10 indicate novel functionalities in habitats with little or no light. Quantification of protein 11 abundance in the various environments supports our findings that bacteria utilize light for 12 sensing, repair, and adaptation far more widely than previously thought. While the discoveries 13 illustrate the opportunities in function discovery, we also discuss the immense conceptual and 14 practical challenges that come along with this new type of data.