Strategies for the Design and Discovery of Novel Antibiotics using Genetic Engineering and Genome Mining

Abstract

Most bioactive natural products currently known are synthesized by members of the Actinomycetales order. The development of genetic engineering provides novel genetic tools for the modification of known antibiotics and other bioactive compounds to generate derivatives with improved therapeutic properties. This new technology, named combinatorial biosynthesis, is able of introducing structural modifications in bioactive compounds not easily accessible by chemical means. Furthermore, progress in genome sequencing in this group of microorganisms shows that actinomycetes have a greater potential of synthesizing bioactive compounds than was anticipated. Each genome sequenced shows the presence of 18-37 gene clusters potentially directing the biosynthesis of bioactive compounds that have not been previously identified. Novel strategies are being developed to activate these cryptic or silent gene clusters in these microorganisms, allowing the identification of novel potentially bioactive compounds. This chapter will revise the state of the art in this field of research.

Genome Mining as New Challenge in Natural Products Discovery

“…These techniques, together with bioinformatic approaches, have shown that the ability of organisms (particularly microorganisms) to produce bioactive natural products has been underestimated [25]. These organisms have been deeper explored through the sequencing of their genome and the application of genome mining approaches [26]. Genome analysis has shed light the presence of numerous biosynthetic gene clusters that could be involved in the synthesis of other secondary metabolites defined cryptic or orphan for their unknown origin [25].…”

“…The importance of genome mining is based on the urgent need to discover new drug entities due to the increased incidence of severe diseases (such as cancer) and the reduced efficacy of existing drugs [27]. Furthermore, the biosynthetic gene clusters contain elements that can be used to increase the production of both natural and engineered products by promoting costs reduction and their commercial use [26].…”

“…As reported in Wohlleben et al [6], a great disadvantage of genome mining is that only known biosynthetic gene clusters can be identified [29]. Moreover, with this approach, it is not possible to predict the biological activities of the natural products identified [26]. However, genome mining is still an evolving technique [29], in fact, scientists are trying to improve this bioinformatic tool in order to reduce the limits of this approach.…”

“…Gene inactivation involves the creation of a mutant organism, in which the biosynthetic gene cluster becomes inactive, thus eliminating the production of metabolites. The comparison between mutant organisms can be made by high-performance liquid chromatography/mass spectrometry (HPLC-MS), revealing the natural product absent in the mutant organism [26]. Therefore, gene inactivation needs as evidence of cluster involvement in compound biosynthesis [24].…”

Actinobactérias de biomas brasileiros: biodiversidade e potencial de uso na agricultura

“…O mapeamento do genoma consiste em descrever o conjunto gênico presente em todos DNA do organismo alvo. Nos anos recentes, esta técnica é aplicada com grande sucesso no grupo de actinobactérias, especificamente o gênero Streptomyces e tornou-se uma abordagem nova e rápida para identificar genes anteriormente desconhecidos (Olano et al, 2014;Ochi, 2016).…”