title: A prevalent peptide-binding domain guides ribosomal natural product biosynthesis.
abstract: Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a rapidly growing class of natural products. RiPP precursor peptides can undergo extensive enzymatic tailoring to yield structurally and functionally diverse products, and their biosynthetic logic makes them attractive bioengineering targets. Recent work suggests that unrelated RiPP-modifying enzymes contain structurally similar precursor peptide-binding domains. Using profile hidden Markov model comparisons, we discovered related and previously unrecognized peptide-binding domains in proteins spanning the majority of known prokaryotic RiPP classes, and we named this conserved domain the RiPP precursor peptide recognition element (RRE). Through binding studies we verified RRE's roles for three distinct RiPP classes: linear azole-containing peptides, thiopeptides and lasso peptides. Because numerous RiPP biosynthetic enzymes act on peptide substrates, our findings have powerful predictive value as to which protein(s) drive substrate binding, thereby laying a foundation for further characterization of RiPP biosynthetic pathways and the rational engineering of new peptide-binding activities.
authors.affiliation: 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Brandon J
authors.initials: BJ
authors.lastname: Burkhart
authors.affiliation: 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Graham A
authors.initials: GA
authors.lastname: Hudson
authors.affiliation: 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Kyle L
authors.initials: KL
authors.lastname: Dunbar
authors.affiliation: 1] Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [2] Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA. [3] Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Mitchell
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001430:Bacteriocins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D001688:Biological Products / Q000737:chemistry / Q000378:metabolism*; D015870:Gene Expression; D008390:Markov Chains; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D011485:Protein Binding; D014176:Protein Biosynthesis; D011499:Protein Processing, Post-Translational; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D001430:Bacteriocins; D001688:Biological Products; D010455:Peptides; C020411:microcin