Genome mining for drug discovery: cyclic lipopeptides related to daptomycin

Abstract

The cyclic lipopeptide antibiotics structurally-related to daptomycin were first reported in the 1950s. Several have common lipopeptide initiation, elongation, and termination mechanisms. Initiation requires the use of a fatty-acyl AMP ligase (FAAL), a free-standing acyl carrier protein (ACP), and a specialized condensation (CIII) domain on the first NRPS elongation module to couple the long chain fatty acid to the first amino acid. Termination is carried out by dimodular NRPS that contains a terminal thioesterase (Te) domain (CAT-CATTe). Lipopeptide BGCs also encode ABC transporters, apparently for export and resistance. The use of this mechanism of initiation, elongation, and termination, coupled with molecular target-agnostic resistance, has provided a unique basis for robust natural and experimental combinatorial biosynthesis to generate a large variety of structurally-related compounds, some with altered or different antibacterial mechanisms of action. The FAAL, ACP, and dimodular NRPS genes were used as molecular beacons to identify phylogenetically-related BGCs by BLASTp analysis of finished and draft genome sequences. These and other molecular beacons have identified: (i) known, but previously unsequenced lipopeptide BGCs in draft genomes; (ii) a new daptomycin family BGC in a draft genome of Streptomyces sedi; and (iii) novel lipopeptide BGCs in the finished genome of Streptomyces ambofaciens and the draft genome of Streptomyces zhaozhouensis.

Genome mining for drug discovery: progress at the front end

“…This was a major contributor to diminishing returns on investment that were not sustainable. An important advantage of microbial genome mining is the ability to focus on compounds predicted to be truly novel, and on derivatives of highly active molecules, based initially on bioinformatic analysis alone (Bachmann et al, 2014 ; Baltz, 2019 , 2021 ). To accomplish this efficiently, it is important to have publicly available sequences from microbes that produce known compounds to serve as an open resource for rapid bioinformatic dereplication of known BGCs.…”

“…To accomplish this efficiently, it is important to have publicly available sequences from microbes that produce known compounds to serve as an open resource for rapid bioinformatic dereplication of known BGCs. In addition, such a database can serve as a source for mining other new and novel BGCs encoded by the reference genomes, and to support ongoing studies on the evolution and ecology of BGCs that can be applied to synthetic biology and combinatorial biosynthesis approaches to drug discovery (Baltz, 2018 , 2021 ; Chevrette & Currie, 2019 ; Chevrette et al, 2019 ; Chevrette et al, 2020 ; Culp et al, 2020 ; van Bergeijk et al, 2020 ; Waglechner et al, 2019 ).…”

“…It is approved to treat complicated skin and skin structure infections (SSSI) caused by Gram-positive pathogens, and S. aureus bacteremia, including right-sided endocarditis (Eisenstein et al, 2010 ). The biosynthesis of daptomycin is well understood, and many derivatives have been produced by semisynthesis and combinatorial biosynthesis (Baltz, 2014 , 2021 ). The phylogenetic relationships between diverse lipopeptides have revealed that they employ biosynthetic mechanisms highly suitable for natural evolution, laboratory-based combinatorial biosynthesis, and divergence in the mechanism of action (Baltz, 2021 ).…”

“…In recent years, the discovery of new and novel natural products has been accelerating by advancements in the microbial genome mining processes (Bachmann et al, 2014 ; Baltz, 2017a , 2017c , 2019 ; Foulston, 2019 ; Kalkreuter et al, 2020 ; Mitousis et al, 2020 ; Musiol-Kroll et al, 2019 ). Genome mining also provides an ever-expanding set of genetic parts and devices for synthetic biology approaches to facilitate combinatorial biosynthesis of novel variants of biologically active secondary metabolites, such as antibiotics (Baltz, 2018 , 2019 , 2021 ; Katz et al, 2018 ; Whitford et al, 2021 ; Yuzawa et al, 2018 ). In this perspective, I focus on a few key advancements and opportunities at the front end of the genome mining discovery process and limit my discussions to bacteria, primarily actinomycetes.…”

Introduction to the special issue: “Natural Product Discovery and Development in the Genomic Era: 2021”

“…Shen and co-workers report the discovery of the ammosesters, a new sub-family of the ammosamide family of pyrroloquinoline alkaloids, by mining the Streptomyces uncialis DCA2648 genome, and comparative analysis of the ammosamide and ammosester BGCs support the use of a scaffold peptide as an emerging paradigm for the biosynthesis of the pyrroloquinoline family of natural products (Luo et al, 2021 ). Richard Baltz highlights how the characteristic features of nonribosomal peptide synthetase (NRPS) BGCs could be exploited as molecular beacons to identify phylogenetically related BGCs encoding new natural products by BLASTp analysis of finished and draft genome sequences, as exemplified by novel lipopeptide BGCs including a new daptomycin family BGC in a draft genome of Streptomyces sedi (Baltz, 2021 ). Finally, Yoon and co-workers teach us how to further enhance clavulanic acid production titer in an industrial strain of Streptomyces clavuligerus by optimizing glycerol utilization, demonstrating reporter-guided mutant selection as an efficient method for further titer improvement of randomly mutagenized industrial strains (Shin et al, 2021 ).…”