RadicalSAM.org: A Resource to Interpret Sequence-Function Space and Discover New Radical SAM Enzyme Chemistry

Abstract

The radical SAM superfamily (RSS), arguably the most functionally diverse enzyme superfamily, is also one of the largest with ∼700 K members currently in the UniProt database. The vast majority of the members have uncharacterized enzymatic activities and metabolic functions. In this Perspective, we describe RadicalSAM.org, a new web-based resource that enables a user-friendly genomic enzymology strategy to explore sequence-function space in the RSS. The resource attempts to enable identification of isofunctional groups of radical SAM enzymes using sequence similarity networks (SSNs) and the genome context of the bacterial, archaeal, and fungal members provided by genome neighborhood diagrams (GNDs). Enzymatic activities and in vivo functions frequently can be inferred from genome context given the tendency for genes of related function to be clustered. We invite the scientific community to use RadicalSAM.org to (i) guide their experimental studies to discover new enzymatic activities and metabolic functions, (ii) contribute experimentally verified annotations to RadicalSAM.org to enhance the ability to predict novel activities and functions, and (iii) provide suggestions for improving this resource.

Diverse Protein Architectures and α-N-Methylation Patterns Define Split Borosin RiPP Biosynthetic Gene Clusters

“…Radical SAM enzymes are a particularly diverse set of enzymes catalyzing a wide array of chemically difficult biosynthetic transformations. 33 Members of the radical SAM family PF04055 have been found in a wide variety of putative 34 and known 35 RiPP families that include the bottromycins, 36 sactipeptides, 37 ranthipeptides, 38 streptide, 39,40 and PQQ. 41 Despite few highly represented biosynthetic enzyme families found across all split borosin BGCs, individual borosin pathways can encode a number of putative posttranslationally modifying enzymes.…”

Identification of a poly-cyclopropylglycine–containing peptide via bioinformatic mapping of radical S-adenosylmethionine enzymes

“…Currently, most rSAM-dependent RiPPs that have been characterized to-date are derived from Haft and Basu's initial bioinformatic study (10). While many pathways remain uncharacterized from their study, the advancement of bioinformatic toolsets, such as EFI-EST and EFI-GNT, and the recently launched radicalSAM.org (39) has provided opportunities to expand the search for rSAM-dependent RiPPs. For instance, the EST/GNT approach has been used extensively by the Seyedsayamdost group to expand the streptide family of quorum-sensing molecules into new rotapeptides, triglycines, and streptosactins to name a few (33,40,41).…”

A roadmap for the functional annotation of protein families: a community perspective

“…This requires cycles of increasing similarity cutoff changes and subsequent analyses by the user to choose cutoffs that are case-dependent and involve much trial and error. Recent developments of the tools show how a precomputed analysis of the Radical SAM family, one the most chemically diverse superfamilies studied to date, can greatly facilitate the correct annotation of Radical SAM subgroups with known functions as well as guide the characterization of the ones that remain to be discovered ( 54 ). Current issues of scale limit the systematic use of precomputed SSNs for all protein families, but sequence-embedding tools that do not rely on exhaustive pairwise comparisons were discussed or presented by three workshop participants: Claire McWhite (Princeton University), Christian Dallago (Technical University of Munich) and Lucie Colwell (Cambridge University).…”