New Insights into the Biosynthetic Logic of Ribosomally Synthesized and Post- translationally Modified Peptide Natural Products  Manuel A. Ortega, Wilfred A. van der Donk  Cell Chemical Biology  Volume 23, Issue 1, Pages 31-44 (January 2016) DOI: 10.1016/j.chembiol.2015.11.012 Copyright © 2016 Elsevier Ltd Terms and Conditions

Cell Chemical Biology 2016 23, 31-44DOI: (10. 1016/j. chembiol. 2015 Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 1 A Window into RiPP Biosynthesis (A) Schematic RiPP biosynthetic pathway. Representative RiPP biosynthetic gene cluster wherein each gene encodes a biosynthetic enzyme color-coded by the modification it catalyzes. Dotted circles represent amino acids within the leader peptide. Full circles represent amino acids within the core region. (B) Chemical structures of select RiPP subfamily members. Structural features defining a particular RiPP subfamily are shown in blue. Additional PTMs are shown in red. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 2 Overview of PTMs in Lasso Peptides, Cyanobactins, and Lanthipeptides (A) Proposed biosynthetic scheme during the maturation of the lasso peptide microcin J25. Leader peptide is shown as dotted circles; core peptide is shown as a line. (B) PTMs often present in cyanobactins. (C) Proposed mechanism for the formation of azolines in cyanobactins catalyzed by YcaO-like cyclodehydratases. (D) Common PTMs found in lanthipeptides. (E and F) Proposed dehydration mechanism employed by (E) class I lanthipeptide dehydratases and (F) class II–IV lanthionine synthetases. (G) Proposed cyclization mechanism in lanthipeptides. Xn, connecting peptide. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 3 Overview of PTMs in Thiopeptides, Sactipeptides, and Streptide (A) Putative macrocyclization mechanism involved in the generation of the characteristic central six-membered nitrogen-containing heterocycle in thiopeptides. To date no direct evidence favoring either a concerted or stepwise mechanism has been provided. (B) Proposed steps involved in the generation of MIA during nosiheptide biosynthesis catalyzed by NosL. (C) Trp methylation catalyzed by TsrM during thiostrepton biosynthesis. (D and E) Overview of SAM-dependent transformations during (D) sactipeptide and (E) streptide biosynthesis. Xn, connecting peptide. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 4 Leader-Peptide Removal by RiPP PCATs (A) General domain architecture of PCAT enzymes. (B) Proposed model of leader-peptide removal with concomitant transport catalyzed by PCATs. Cartoon representing the complex in its ATP-free (left) and ATP-bound (right) forms. Figure adapted from Lin et al. (2015). TMD, transmembrane domain; NBD, nucleotide-binding domain. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 5 Recognition of the Leader Peptide by the RiPP Biosynthetic Machinery (A and B) Cartoon (top) and surface (bottom) representation of the wHTH motif in (A) NisB in complex with NisA (PDB ID 4WD9) and (B) LynD in complex with PatE′ (PDB ID 4V1T). PatE′ and NisA leader peptides are shown in red (top) or green (bottom). (C and D) Cartoon representation of (C) PqqD (PDB ID 3G2B) and of (D) the putative leader peptide binding site in CylM (PDB ID 5DZT). In all structures α helices are shown in cyan, and β sheets are shown in magenta. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions

Figure 6 General Strategy for RiPP Genome Mining and Structural Characterization BGC, biosynthetic gene cluster. Cell Chemical Biology 2016 23, 31-44DOI: (10.1016/j.chembiol.2015.11.012) Copyright © 2016 Elsevier Ltd Terms and Conditions