bioRxiv Science⌕ Search

Biology subjects

Padhi, C.

Publications and source records attributed to Padhi, C..

4 recordsLinked to original sources

Late-Stage Posttranslational Assembly of Fosfazinomycins

The fosfazinomycins are phosphonate natural products with antifungal activity. Their main scaffold is composed of a phosphonate moiety attached to the carboxylate of arginine via a hydrazine linkage. Previous studies have elucidated a convergent biosynthetic pathway that independently assembles phosphonate and hydrazine synthons, but how these building blocks are then connected could not be determined. In this work, we provide the final missing steps in fosfazinomycin biosynthesis by revealing an unexpected engagement of biosynthetic machinery that is typically involved in ribosomally synthesized and post-translationally modified peptides (RiPPs). An asparagine synthetase-like (AS-like) enzyme catalyzes the installation of hydrazine onto the carboxylate of Arg at the C-terminus of a short ribosomally synthesized precursor peptide. The terminal nitrogen of the resulting peptide hydrazide is methylated, and the phosphonate moiety is activated to a triphosphate-like intermediate through two separate kinase catalyzed phosphorylation steps. A nucleotidyl transferase then catalyzes the ligation of the two fragments to generate the mature fosfazinomycin scaffold on a peptide. Aminopeptidase cleavage of this peptide then yields fosfazinomycin B (fosB), which serves as substrate for a valinyl-tRNA dependent reaction to afford fosfazinomycin A (fosA). This work demonstrates an unprecedented example of the convergence of RiPP and phosphonate biosynthetic logic, an enzymatic route to peptide hydrazides that are widely used in peptide ligation chemistry, and an unusual activation sequence for conjugation of phosphonates.

biochemistry↗

Substrate-dependent crosslinking by the cytochrome P450 from aminopyruvatide biosynthesis

Cytochrome P450s catalyze an array of reactions including crosslinking of aromatic side chains in the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs). ApyO is a cytochrome P450 that forms a C-C bond between two tyrosines in a YLY motif in the substrate ApyA, the precursor peptide of the RiPP aminopyruvatide. We utilized cell-free translation to generate ApyA variants and probe the substrate tolerance of ApyO. Through Alphafold-based modelling and in vitro assays, we show that ApyO accepts the 10 C-terminal residues of ApyA and requires a conserved Arg/Lys in the substrate. Inspired by substrate sequences in orthologous biosynthetic gene clusters, we substituted one of the tyrosine residues with a tryptophan and observed that ApyO catalyzed formation of an N-C bond between the indole of Trp and C{epsilon}2 of Tyr. ApyO unexpectedly catalyzed formation of a C-O bond between the two tyrosine residues when we substituted the leucine residue in the YLY motif with tyrosine or tryptophan. A peptide containing a biaryl linkage and C-terminal aminopyruvate displayed sub-nanomolar inhibition of select proteases with the aminopyruvate group critical for activity. Overall, this study demonstrates plasticity in the manner of macrocyclization catalyzed by the P450 ApyO.

biochemistry↗

Discovery and Biosynthesis of Nitrilobacillins by Post-translational Introduction of C-Terminal Nitrile Groups

Nitrile-containing natural products are produced in all kingdoms of life. Despite the wide application of nitrile-containing peptide scaffolds in medicinal chemistry, the presence of the nitrile group is unprecedented in ribosomally synthesized and post-translationally modified peptides (RiPPs). In this work, we report the identification and characterization of a RiPP biosynthetic gene cluster (BGC), where an asparagine synthetase-like (AS-like) protein encoded in the BGC converts the C-terminal carboxylate of the precursor peptide to a nitrile. Furthermore, a multinuclear nonheme iron-dependent oxidative enzyme (MNIO) and an -ketoglutarate-dependent HExxH motif-containing enzyme (KG-HExxH) perform stereoselective {beta}-hydroxylation of aspartate and proline residues, respectively. Structure prediction-guided mechanistic evaluation of the nitrile synthetase provided insights into the possible mechanism of catalysis. These findings extend our understanding of the structural diversity of RiPPs and demonstrate the catalytic versatility of AS-like enzymes in natural product biosynthesis.

biochemistry↗

Biosynthesis of Macrocyclic Peptides by Formation and Crosslinking of ortho-Tyrosines

Ribosomally synthesized and posttranslationally modified peptides (RiPPs) are a growing class of natural products that possess many activities that are of potential translational interest. Multinuclear non-heme iron dependent oxidative enzymes (MNIOs), until recently termed domain of unknown function 692 (DUF692), have been gaining interest because of their involvement in a range of biochemical reactions that are remarkable from a chemical perspective. Over 13,500 putative MNIO-encoding biosynthetic gene clusters (BGCs) have been identified by sequence similarity networks (SSNs). In this study, we identified a set of precursor peptides containing a conserved FHAFRF-motif in MNIO-encoding BGCs. These BGCs follow a conserved synteny with genes encoding an MNIO, a RiPP recognition element (RRE)-containing partner protein, an arginase, and a B12-dependent radical SAM enzyme (rSAM). Using heterologous reconstitution of a representative BGC from Peribacillus simplex (pbs cluster) in E. coli, we demonstrated that the MNIO in conjunction with the partner protein catalyzes ortho-hydroxylation of each of the phenylalanine residues in the conserved FRF-motif, the arginase forms an ornithine by deguanidination of the arginine in the motif, and the B12-rSAM crosslinks the ortho-Tyr side side chains by a C-C linkage forming a novel macrocyclic molecule. Substrate scope studies suggested tolerance of the MNIO and the B12-rSAM towards substituting the Phe residues with tyrosines in the conserved motif with the position of hydroxylation and crosslinking being maintained. Overall, this study expands the diverse array of posttranslational modifications catalyzed by MNIOs and B12-rSAM enzymes. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/647296v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@37d9c8org.highwire.dtl.DTLVardef@baf547org.highwire.dtl.DTLVardef@3d0ed8org.highwire.dtl.DTLVardef@99aaee_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗