Cytochromes P450 involved in bacterial RiPP biosyntheses

Abstract

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a large class of secondary metabolites that have garnered scientific attention due to their complex scaffolds with potential roles in medicine, agriculture, and chemical ecology. RiPPs derive from the cleavage of ribosomally-synthesized proteins and the additional modifications, catalyzed by various enzymes to alter the peptide backbone or side chains. Of these enzymes, cytochromes P450 are a superfamily of heme-thiolate proteins involved in many metabolic pathways, including RiPP biosyntheses. In this review, we focus our discussion on cytochromes P450 involved in RiPP pathways and the unique chemical transformations they mediate. Previous studies have revealed a wealth of cytochromes P450 distributed across all domains of life. While the number of characterized cytochromes P450 involved in RiPP biosyntheses is relatively small, they catalyze various enzymatic reactions such as C-C or C-N bond formation. Formation of some RiPPs is catalyzed by more than one cytochrome P450, enabling structural diversity. With the continuous improvement of the bioinformatic tools for RiPP prediction and advancement in synthetic biology techniques, it is expected that further cytochrome P450-mediated RiPP biosynthetic pathways will be discovered.

Structural Insights into a Side Chain Cross-Linking Biarylitide P450 from RiPP Biosynthesis

“…12,13 More recently, ribosomal biosynthesis pathways (Ribosomally synthesized and post-translationally modified peptides (RiPPs)) involving P450 cross-linking reactions have been widely reported and investigated, showing high levels of diversity in the reactions catalyzed and the substrates accepted by this intriguing group of P450s. 14 While many of these new classes of P450s utilize large leader sequences relative to their smaller core peptides, the biarylitides 15 (and related myxarylins) 16 are remarkably atom efficient in their use of a two amino acid leader appended to a three amino acid core peptide. Biochemical characterization has shown that the biarylitide P450s possess the ability to generate alternate (C− C, C−N) cross-links within their Tyr-Xaa-His cores (where Xaa can be highly varied) and furthermore that these enzymes can also tolerate a range of modifications within the cross-link and even the replacement of the terminal His residue with Trp.…”

“…This is particularly notable in the biosynthesis of several important classes of nonribosomal peptides (NRPs), including the glycopeptide antibiotics (GPAs, such as vancomycin, teicoplanin and corbamycin) and arylomycin . While P450s from NRP pathways have been characterized, − and in the case of GPAs also in complex with their essential recruitment domains, , none of these P450s have been in a substrate bound form, making an assessment of the mechanism utilized and the substrate binding mode employed by these enzymes elusive. , More recently, ribosomal biosynthesis pathways (Ribosomally synthesized and post-translationally modified peptides (RiPPs)) involving P450 cross-linking reactions have been widely reported and investigated, showing high levels of diversity in the reactions catalyzed and the substrates accepted by this intriguing group of P450s . While many of these new classes of P450s utilize large leader sequences relative to their smaller core peptides, the biarylitides (and related myxarylins) are remarkably atom efficient in their use of a two amino acid leader appended to a three amino acid core peptide.…”

Bioinformatics-guided discovery of biaryl-linked lasso peptides

“…One Nocardia BGC contained a member of protein family PF00067, 12 a predicted cytochrome P450 protein. While P450-encoding genes are relatively rare in bacterial RiPP BGCs, 13 they have yet to be reported in a lasso peptide BGC. Since RiPP-associated P450 proteins perform versatile and complex oxidative transformations, 13,14 we envisioned such BGCs would yield a new type of lasso peptide.…”

“…While P450-encoding genes are relatively rare in bacterial RiPP BGCs, 13 they have yet to be reported in a lasso peptide BGC. Since RiPP-associated P450 proteins perform versatile and complex oxidative transformations, 13,14 we envisioned such BGCs would yield a new type of lasso peptide. Thus, we characterized the products of this pathway, termed the nocapeptins, given the origin was Nocardia terpenica (taxonomic order: Corynebacteriales).…”

Cytochromes P450 Associated with the Biosyntheses of Ribosomally Synthesized and Post-translationally Modified Peptides

“…While P450s impress by their tremendously functional versatility that is involved in the biosynthesis of abundant secondary metabolites including polyketides (PKs), nonribosomal peptide (NRPs), cyclodipeptides (CDPs), and terpenes (Figure ), the involvement of P450s in the biosynthesis of RiPPs is comparatively limited and few reviews have been summarized for this field to my knowledge (Table ). While this Review was under preparation, Kunakom et al published an excellent review about P450s involved in bacterial RiPP biosynthesis, with emphases on the distribution of P450s in bacterial genomes and the biosyntheses of atropitides, biarylitides, cittlins, as well as nocathiacin that harbors rich P450s . Herein, this Review provides a more comprehensive description of all the P450s with functionalities in the PTMs of RiPPs to date according to different classifications (Table ), including P450s involved in some eukaryotic RiPP biosyntheses.…”