Chemical Elicitors Induce Rare Bioactive Secondary Metabolites in Deep-Sea Bacteria under Laboratory Conditions.

Rafael De Felício,Cristina Freitas Bazzano,Gina Polo Infante,Luciane A C Tonon,Patricia Ballone,Luciana S Paradela,Guilherme P Telles,Renata Sigrist,Andréa Dessen,Marcus Adonai Castro Da Silva,Henrique Niero,Arthur Zanetti Nunes Fernandes,Fernanda Rodrigues-Costa,Sandra Martha Gomes Dias,Luiz F G Alves,Daniela Barretto Barbosa Trivella,Andre Oliveira De Souza Lima,Renna Karoline Eloi Costa

doi:10.3390/metabo11020107

Abstract

Bacterial genome sequencing has revealed a vast number of novel biosynthetic gene clusters (BGC) with potential to produce bioactive natural products. However, the biosynthesis of secondary metabolites by bacteria is often silenced under laboratory conditions, limiting the controlled expression of natural products. Here we describe an integrated methodology for the construction and screening of an elicited and pre-fractionated library of marine bacteria. In this pilot study, chemical elicitors were evaluated to mimic the natural environment and to induce the expression of cryptic BGCs in deep-sea bacteria. By integrating high-resolution untargeted metabolomics with cheminformatics analyses, it was possible to visualize, mine, identify and map the chemical and biological space of the elicited bacterial metabolites. The results show that elicited bacterial metabolites correspond to ~45% of the compounds produced under laboratory conditions. In addition, the elicited chemical space is novel (~70% of the elicited compounds) or concentrated in the chemical space of drugs. Fractionation of the crude extracts further evidenced minor compounds (~90% of the collection) and the detection of biological activity. This pilot work pinpoints strategies for constructing and evaluating chemically diverse bacterial natural product libraries towards the identification of novel bacterial metabolites in natural product-based drug discovery pipelines.

Highlights

Secondary metabolites, known as natural products, are complex and threedimensionally oriented molecules that belong to diverse groups of organic compounds, which expand across the chemical space of known molecules [1]
This workflow was directed towards the induction of cryptic biosynthetic gene clusters (BGC) in deep-sea bacteria under laboratory conditions, aiming to appraise the vast chemical diversity that can be provided by a bacterial collection
Bacteria were grown in the presence or absence of the chemical elicitors using large-scale cultivation (Section 2.1.3)

Summary

Introduction

Known as natural products, are complex and threedimensionally oriented molecules that belong to diverse groups of organic compounds, which expand across the chemical space of known molecules [1]. To increase survival rates under these conditions, microorganisms adopt several strategies, such as the production of secondary metabolites to counteract physicochemical changes in the environment (e.g., pigments), as well as bioactive secondary metabolites to combat their competitors in their native habitat Examples of such metabolites are penicillin and epoxyketone peptides. The epoxyketone peptides eponemycin [5] and epoxomicin [6] are produced by actinomycete bacteria, selectively binding to the active sites of the proteasome, an important proteolytic protein complex of eukaryotic cells, essential for protein homeostasis [7,8] Along with their antifungal properties, proteasome inhibitors of bacterial origin have been crucial for inspiring the development of second (e.g., carfilzomib/Kyprolis® —derived from epoxomicin [6])

Methods

Results

Discussion

Conclusion