Diversity of Monomers in Nonribosomal Peptides: towards the Prediction of Origin and Biological Activity

Nonribosomal peptides (NRPs) are molecules produced by microorganisms that have a broad spectrum of biological activities and pharmaceutical applications (e.g., antibiotic, immunomodulating, and antitumor activities). One particularity of the NRPs is the biodiversity of their monomers, extending far beyond the 20 proteogenic amino acid residues. Norine, a comprehensive database of NRPs, allowed us to review for the first time the main characteristics of the NRPs and especially their monomer biodiversity. Our analysis highlighted a significant similarity relationship between NRPs synthesized by bacteria and those isolated from metazoa, especially from sponges, supporting the hypothesis that some NRPs isolated from sponges are actually synthesized by symbiotic bacteria rather than by the sponges themselves. A comparison of peptide monomeric compositions as a function of biological activity showed that some monomers are specific to a class of activities. An analysis of the monomer compositions of peptide products predicted from genomic information (metagenomics and high-throughput genome sequencing) or of new peptides detected by mass spectrometry analysis applied to a culture supernatant can provide indications of the origin of a peptide and/or its biological activity.Nonribosomal peptides (NRPs) are molecules produced by microorganisms and synthesized by huge multienzymatic complexes (38, 41), called nonribosomal peptide synthetases (NRPSs). These megaenzymes are organized into modules, one for each amino acid to be built into the peptide product. This is accomplished by division of each catalytic step into specialized semiautonomous domains. The basic set of domains (adenylation, thiolation, and condensation) within a module can be extended by substrate-modifying domains, including domains for substrate epimerization, β hydroxylation, N methylation, and heterocyclic ring formation. The peptide release is catalyzed by a thioesterase domain which can also, in many cases, be involved in an intramolecular reaction leading to a cyclic or partially cyclic peptide or, in fewer cases, in the oligomerization of peptide units (iterative biosynthesis). NRPs show a broad spectrum of biological activities and pharmaceutical applications. They can harbor antimicrobial, immunomodulator, or antitumor activities. Cyclosporine (5), an immunosuppressant drug widely used in organ transplantation, daptomycin (60) (marketed in the United States under the trade name Cubicin), used in the treatment of certain infections caused by Gram-positive bacteria, aminoadipyl-cysteinyl-valine (ACV)-tripeptide, which is the precursor of cephalosporin and penicillin (29), the most famous antibiotic, and also bleomycin (57), used in the treatment of several cancers, are some common examples of NRPs of high therapeutic importance. Two main structural traits distinguish these peptides from ribosomally synthesized peptides: first, their primary structure is more frequently cyclic (partially or totally) branched or polycyclic rather than linear and, second, the biodiversity of monomers incorporated in NRPs goes far beyond the 20 proteogenic amino acids residues. NRP monomers include modified versions of the proteogenic amino acids (e.g., methylated, hydroxylated, and d-forms) but also other monomers, such as, for example, 2-aminoisobutyric acid (Aib), hydroxyphenylglycine (Hpg), and 2,3-dihydroxybenzoic acid (diOH-Bz). However, essential characteristics of this diversity and its relationship with biological functions and producing organisms have been poorly understood until now.The development of the Norine database, the first resource entirely dedicated to NRPs (8, 9), filled this gap. Based on Norine data, we performed the first large-scale analysis of about a thousand peptides which represent a total coverage of more than 10,000 monomer occurrences, revealing the presence of as many as 500 different monomer types. A data-mining analysis of the monomeric compositions of NRPs allowed us to reveal a strong relationship between certain monomeric characteristics of NRPs and their biological function and producing organism. In addition to providing a comprehensive overview of monomeric biodiversity in NRPs, this work demonstrated (i) a dissimilarity of structural properties between bacterial and fungal NRPs; (ii) a significant relationship between NRPs synthesized by bacteria and those isolated from metazoa, especially from sponges, supporting the hypothesis that the peptides isolated from sponges are in reality synthesized by symbiotic bacteria rather than by the sponges themselves; and (iii) a certain monomer specificity to a class of biological activities. Those observations are supported by successful statistical predictions of biological activities of NRPs based on their monomeric compositions.