Prospecting for new bacterial metabolites: a glossary of approaches for inducing, activating and upregulating the biosynthesis of bacterial cryptic or silent natural products

Abstract

Over the centuries, microbial secondary metabolites have played a central role in the treatment of human diseases and have revolutionised the pharmaceutical industry. With the increasing number of sequenced microbial genomes revealing a plethora of novel biosynthetic genes, natural product drug discovery is entering an exciting second golden age. Here, we provide a concise overview as an introductory guide to the main methods employed to unlock or up-regulate these so called 'cryptic', 'silent' and 'orphan' gene clusters, and increase the production of the encoded natural product. With a predominant focus on bacterial natural products we will discuss the importance of the bioinformatics approach for genome mining, the use of first different and simple culturing techniques and then the application of genetic engineering to unlock the microbial treasure trove.

Biosynthetic Pathway Connects Cryptic Ribosomally Synthesized Posttranslationally Modified Peptide Genes with Pyrroloquinoline Alkaloids

“…(Bentley et al, 2002; Udwary et al, 2007; Weber, 2014; Zarins-Tutt et al, 2015; Ziemert et al, 2016) This latent capacity is often encoded within so-called ‘orphaned gene clusters’ for which the chemical product has not been identified. Yet, for many of these orphaned biosynthetic gene clusters (BGCs), gross structure predictions are possible in the absence of chemical information, especially for the most well characterized biosynthetic systems, such as polyketides, and non-ribosomal and ribosomal peptides.…”

Predominately Uncultured Microbes as Sources of Bioactive Agents

“…These include, but are not limited to: discussion of eliciting secondary metabolism in actinomycetes (Seyedsayamdost et al, 2012; Abdelmohsen et al, 2015; Rutledge and Challis, 2015); methodologies for determining the compounds expressed (Adnani et al, 2014; Luzzatto-Knaan et al, 2015; Medema and Fischbach, 2015; Mohimani and Pevzner, 2016); analyses of the biosynthetic clusters identified in fungi to published natural product structures (Li et al, 2016b); small-scale plate-based techniques for fungal co-culture (Bertrand et al, 2014); on-demand production of secondary metabolites (Bode et al, 2015); mixed culture of endophytes (Chagas et al, 2013); metabolomics in induced cultures (Derewacz et al, 2015; van der Lee and Medema, 2016; Zhang et al, 2016a,b; Ziemert et al, 2016); use of synthetic biological techniques to further expand the chemical biodiversity discovered (Smanski et al, 2016); and a recent review of the array of approaches to study such cryptic cluster expression by Zarins-Tutt et al (2016).…”

Omics-based natural product discovery and the lexicon of genome mining

“…Considerable advances have been made in the activation of silent BGCs[22,24,54,55] using techniques such as co-cultivation[56] or the addition of small molecule inducers[57,58]. While these methods have proven useful, it’s also possible that many BGCs are active yet their small molecule products are simply missed due to the extraction methods or analytical techniques employed (Figure 1).…”