Genome Mining Methods Research Articles

The evolution of genome mining in microbes - a review.

Covering: 2006 to 2016The computational mining of genomes has become an important part in the discovery of novel natural products as drug leads. Thousands of bacterial genome sequences are publically available these days containing an even larger number and diversity of secondary metabolite gene clusters that await linkage to their encoded natural products. With the development of high-throughput sequencing methods and the wealth of DNA data available, a variety of genome mining methods and tools have been developed to guide discovery and characterisation of these compounds. This article reviews the development of these computational approaches during the last decade and shows how the revolution of next generation sequencing methods has led to an evolution of various genome mining approaches, techniques and tools. After a short introduction and brief overview of important milestones, this article will focus on the different approaches of mining genomes for secondary metabolites, from detecting biosynthetic genes to resistance based methods and "evo-mining" strategies including a short evaluation of the impact of the development of genome mining methods and tools on the field of natural products and microbial ecology.

Discovery of a new Fe-type nitrile hydratase efficiently hydrating aliphatic and aromatic nitriles by genome mining

Microbial nitrile hydratases (NHases) are important industrial catalysts to produce valuable amides. However, only some NHase genes have been reported and studied at the molecular level. In this study, we developed a genome mining method to discover Fe-type NHases from GenBank. The putative NHase gene from Pseudomonas putida F1 was cloned and functionally expressed in Escherichia coli BL21 (DE3) by assisting of a putative activator gene adjacent to β-subunit region. Three recombinant plasmids containing NHase gene or the activator gene were designed and constructed. Maximal enzyme activity was obtained when the structural and activator genes were transcribed as one unit in plasmid pCDFDuet-1 at 18 °C. However, the expressed product did not show any NHase activity when the downstream activator gene was ignored, and the product completely existed in insoluble inclusion body. The activator gene might be involved in protein folding of the α- and β-subunits of NHase. In addition, the Fe-type NHase exhibited broad substrate specificity. The enzyme can efficiently hydrate aromatic nitriles, such as 3-cyanopyridine, 4-cyanopyridine, and benzonitrile, asides from aliphatic nitriles preferentially. Therefore, the recombinant NHase shows potential applications in some amides preparation.

Expediting natural product discovery through genomics

Natural product chemicals have historically been discovered based on their molecular and biological properties. With the ease and affordability of genome sequencing today, a new era in natural product discovery is unfolding in which genomics and biosynthesis are together fostering new innovations in compound discovery. This orthogonal discovery approach takes advantage of the biosynthetic potential of a genome-sequenced organism to design hypothesis-driven experiments to uncover new chemical entities. Realizing that mass spectrometry-induced fragmentation of peptidic and carbohydrate-based molecules yields amino acid and sugar monomers that directly correlate as biosynthetic building blocks, we developed two complementary mass spectrometry-guided genome mining methods that connect diverse peptides and sugar-based metabolites directly to their biosynthetic gene clusters. In this lecture I will introduce peptidogenomics (Nat. Chem. Biol., 7, 794–802, 2011) and glycosogenomics as powerful new discovery methods that iteratively match de novo MSn structures to genomics-based structures following current biosynthetic logic. Several novel microbial natural products will be presented to illustrate the unbiased flexibility of this concept that has the potential for automating the genome mining process.

Heavy Tools for Genome Mining

In this issue of Chemistry & Biology, Gross et al. report development of a novel genome mining method for isolating products of orphan biosynthetic gene clusters, and the application of this method to the isolation of orfamide A, a novel cyclic lipopeptide.