In silico methods for linking genes and secondary metabolites: The way forward

Abstract

In silico methods for linking genomic space to chemical space have played a crucial role in genomics driven discovery of new natural products as well as biosynthesis of altered natural products by engineering of biosynthetic pathways. Here we give an overview of available computational tools and then briefly describe a novel computational framework, namely retro-biosynthetic enumeration of biosynthetic reactions, which can add to the repertoire of computational tools available for connecting natural products to their biosynthetic gene clusters. Most of the currently available bioinformatics tools for analysis of secondary metabolite biosynthetic gene clusters utilize the "Genes to Metabolites" approach. In contrast to the "Genes to Metabolites" approach, the "Metabolites to Genes" or retro-biosynthetic approach would involve enumerating the various biochemical transformations or enzymatic reactions which would generate the given chemical moiety starting from a set of precursor molecules and identifying enzymatic domains which can potentially catalyze the enumerated biochemical transformations. In this article, we first give a brief overview of the presently available in silico tools and approaches for analysis of secondary metabolite biosynthetic pathways. We also discuss our preliminary work on development of algorithms for retro-biosynthetic enumeration of biochemical transformations to formulate a novel computational method for identifying genes associated with biosynthesis of a given polyketide or nonribosomal peptide.

Keywords: Biosynthetic gene cluster; Genes to metabolites; Genome mining; Metabolites to genes; Nonribosomal peptides; Polyketides; Retro-biosynthetic enumeration; Secondary metabolite.

Fig. 1

Two approaches for deciphering new biosynthetic pathways. (A) “Forward approach”, where information from genes is used to decipher the biological pathways. “Retro-biosynthetic approach” is where a known product is linked to the genes. Some of the available methods belonging to either approach have been mentioned in boxes. (B) Alternative approaches to connecting genes and metabolites. (Left Panel) Use of module organization in comparison of secondary metabolite gene clusters and prediction of the secondary metabolite synthesized. (Right Panel) Retro-biosynthetic approach for prediction of the gene cluster responsible for biosynthesis of a particular secondary metabolite.

Fig. 2

Schematic representation of retro-biosynthetic enumeration. Schematic diagram representing the main steps involved in the retro-biosynthetic enumeration of reactions leading to a given polyketide and nonribosomal peptide product.

Fig. 3

Examples of generic reactions used for Retro-biosynthetic approach. All possible modules required for the biosynthesis of polyketides and nonribosomal peptides. The second column lists an example reaction catalyzed by each type of module and the generic reaction or reaction rule associated with these modules. Circles indicate change in functional group.

Fig. 4

An example of reaction enumeration. An example of complete reaction enumeration starting from the polyketide – halstoctacosanolide to its starting metabolites using the retro-biosynthetic approach.

Fig. 5

An example of incorrect reaction enumeration starting from the polyketide – monensin. The steps that were wrongly predicted have been highlighted in red.