Plant peptides - redefining an area of ribosomally synthesized and post-translationally modified peptides

Abstract

Covering 1965 to February 2024Plants are prolific peptide chemists and are known to make thousands of different peptidic molecules. These peptides vary dramatically in their size, chemistry, and bioactivity. Despite their differences, all plant peptides to date are biosynthesized as ribosomally synthesized and post-translationally modified peptides (RiPPs). Decades of research in plant RiPP biosynthesis have extended the definition and scope of RiPPs from microbial sources, establishing paradigms and discovering new families of biosynthetic enzymes. The discovery and elucidation of plant peptide pathways is challenging due to repurposing and evolution of housekeeping genes as both precursor peptides and biosynthetic enzymes and due to the low rates of gene clustering in plants. In this review, we highlight the chemistry, biosynthesis, and function of the known RiPP classes from plants and recommend a nomenclature for the recent addition of BURP-domain-derived RiPPs termed burpitides. Burpitides are an emerging family of cyclic plant RiPPs characterized by macrocyclic crosslinks between tyrosine or tryptophan side chains and other amino acid side chains or their peptide backbone that are formed by copper-dependent BURP-domain-containing proteins termed burpitide cyclases. Finally, we review the discovery of plant RiPPs through bioactivity-guided, structure-guided, and gene-guided approaches.

Fig. 1. Plant RiPP chemistry and biosynthesis. (A) RiPP biosynthetic dogma. (B) Representative structures of plant RiPPs and their corresponding size ranges. Peptide mass ranges were determined based on plant peptide databases and studies. (C) Single-core and multi-core precursor peptides of kalata cyclotides. B1 represents kalata B1 core peptide. (D) Precursor proteins with storage, catalytic, and multi-core domains. (E) Fused and split precursor peptides in cyclopeptide alkaloid RiPP biosynthesis. Disulfide bond formation and pyroglutamate formation can occur enzymatically or spontaneously. Abbreviations: PTM – post-translational modification, alb. – albumin, core – core peptide, Leader – leader peptide, Follower – follower peptide.

Fig. 2. Post-translational modifications in plant RiPPs. Terminal modifications are in blue and side-chain-modifications are shown in red. Abbreviations: AEP – asparaginyl endopeptidase, PCY1 – peptide cyclase 1, N-MT – N-methyltransferase, GlnNT – glutamine aminotransferase, PDI – protein disulfide isomerase, TPST – tyrosylprotein sulfotransferase.

Fig. 3. Biosynthesis of cyclotide kalata B1. PDB accession: 1NB1.

Fig. 4. Structures of iconic orbitides and proposed biosynthetic route for segetalin A.

Fig. 5. Biosynthesis of SFTI-1. SSU and LSU are small and large subunits, respectively, of albumin domain. PDB accession: 1JBL.

Fig. 6. Chemical structures and precursor peptides of cysteine-rich plant peptides. (A) Sequences and disulfide bond patterns of representatives of CRP subclasses. Class-defining DSBs and cysteines are highlighted in orange. Solid lines in gray are non-class-defining DSBs to the CRP. Peptide net charges are shown behind species names. (B) Precursor peptides of CRP subclass representatives. (C) Topology diagrams of CRP subclass representatives based on experimentally determined structures.

Fig. 7. Biosynthesis of linear RiPP PSY1.

Fig. 8. Proposed burpitide classification. Representative precursor peptide names are in brackets. Class-defining bonds are highlighted in red, other burpitide cyclase-derived PTMs are highlighted in blue.

Fig. 9. Biosynthetic proposal of lyciumin-type peptides. (A) Proposed formation of lyciumin I and legumenin from AhyBURP (B) Proposed formation of cercic acid from CcaBURP1. (C) The homodimer of AhyBURP, PDB ID 8SY2. Each subunit is in blue, and the core peptides are in orange and colored according to element (oxygen, red; nitrogen, blue). The core peptide and conserved His of BURP-domain-containing proteins are shown as sticks. Main chain atoms are omitted for clarity. (D) Copper-bound structure of AhyBURP, PDB ID 8SY3. The core peptide and conserved Cys and His residues of BURP-domain proteins are shown as sticks (sulfur, yellow). Main chain atoms for Cys-His are omitted for clarity. Dashed lines in (C) and (D) represent disordered regions in the crystal structure.

Fig. 10. Biosynthetic proposal for cyclopeptide alkaloids. (A) Proposed formation of mono- and bicyclic peptide alkaloids from SkrBURP in a fused burpitide pathway. (B) The proposed split burpitide pathway for the production of arabipeptin A. (C) N-terminal modifications observed in cyclopeptide alkaloids: (1) N,N-dimethylation, (2) N-monomethylation, (3) unmodified, (4) N-oxime, (5) N-formylation, (6) cyclized N-methylation (imidizolidine-4-one), (7) deamination (cinnamic acid), (8) Cβ-hydroxylation, C-terminal modifications observed in cyclopeptide alkaloids: (9) p-hydroxy-styrylamine, (10) tyrosine, (11) octopamine, (12) 4-hydroxy-α-aminoacetophenone (13) m-hydroxy-o-methoxy-styrylamine.

Fig. 11. Biosynthetic proposal for stephanotic acid-type burpitides. (A) Proposed biosynthesis of moroidin in Kerria japonica. (B) Proposed biosynthesis of stephanotic acid-[LV] in Cercis canadensis.

Fig. 12. Bouvardin structures.

Fig. 13. Chemtaxonomy of Plant RiPPs. Cladograms annotated with the detected presence of plant RiPPs (A) and specific burpitide types (B).

Jonathan R. Chekan

Lisa S. Mydy

Michael A. Pasquale

Roland D. Kersten