Lessons learned from the transformation of natural product discovery to a genome-driven endeavor

Deane, Caitlin; Mitchell, Douglas A.

doi:10.1007/s10295-013-1361-8

Cited by 20 publications

(16 citation statements)

References 161 publications

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“…Only unambiguous coupling constants were used. Thus, 3 J HNa $ 9 Hz was observed for Ser1, Ile2, Asp4, Gly6, Thr15 and Tyr16. The torsion angles f of these residues were restrained to À120 AE 30 .…”

Section: Nmr-spectroscopic Methodsmentioning

confidence: 94%

“…1,2 While selective screenings for certain bioactivities have been performed in the past by bacterial or fungal fermentations, nowadays the rational approaches gain more ground. 3,4 In particular, genome mining driven predictions and isolations of new compound become more common 5,6 as sequencing costs drop dramatically. Thousands of bacterial genomes have been already sequenced, providing large amounts of data to be analyzed in upcoming research.…”

Section: Introductionmentioning

confidence: 99%

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Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

et al. 2014

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Section: Nmr-spectroscopic Methodsmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

et al. 2014

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“…If we look beyond NRPS and type I PKS pathways, which require substantial coding capacity, it is becoming apparent from recent genome mining successes that many microbes with smaller genomes encode ribosomally synthesized and post-translationally modified peptides (RiPPs) or phosphonates [24, 44, 52]. Perhaps these discoveries will contribute to a more robust drug discovery process in coming years.…”

Section: What Microbes Should Be Mined?mentioning

confidence: 99%

Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

Bachmann

Lanen

Baltz³

2014

Journal of Industrial Microbiology and Biotechnology

250

187

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Microbial genome mining is a rapidly developing approach to discover new and novel secondary metabolites for drug discovery. Many advances have been made in the past decade to facilitate genome mining, and these are reviewed in this Special Issue of the Journal of Industrial Microbiology and Biotechnology. In this Introductory Review, we discuss the concept of genome mining and why it is important for the revitalization of natural product discovery; what microbes show the most promise for focused genome mining; how microbial genomes can be mined; how genome mining can be leveraged with other technologies; how progress on genome mining can be accelerated; and who should fund future progress in this promising field. We direct interested readers to more focused reviews on the individual topics in this Special Issue for more detailed summaries on the current state-of-the-art.

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“…The revolution in genomics, genome mining tools and bioinformatics offers a new opportunity to connect biochemical diversity to the underlying genetic diversity and to analyze the evolutionary events leading to biodiversity (Zotchev et al, 2012 ; Scheffler et al, 2013 ; Deane and Mitchell, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

Mousa

Raizada

2015

Front. Plant Sci.

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The plant is an attractive versatile home for diverse associated microbes. A subset of these microbes produces a diversity of anti-microbial natural products including polyketides, non-ribosomal peptides, terpenoids, heterocylic nitrogenous compounds, volatile compounds, bacteriocins, and lytic enzymes. In recent years, detailed molecular analysis has led to a better understanding of the underlying genetic mechanisms. New genomic and bioinformatic tools have permitted comparisons of orthologous genes between species, leading to predictions of the associated evolutionary mechanisms responsible for diversification at the genetic and corresponding biochemical levels. The purpose of this review is to describe the biodiversity of biosynthetic genes of plant-associated bacteria and fungi that encode selected examples of antimicrobial natural products. For each compound, the target pathogen and biochemical mode of action are described, in order to draw attention to the complexity of these phenomena. We review recent information of the underlying molecular diversity and draw lessons through comparative genomic analysis of the orthologous coding sequences (CDS). We conclude by discussing emerging themes and gaps, discuss the metabolic pathways in the context of the phylogeny and ecology of their microbial hosts, and discuss potential evolutionary mechanisms that led to the diversification of biosynthetic gene clusters.

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Lessons learned from the transformation of natural product discovery to a genome-driven endeavor

Cited by 20 publications

References 161 publications

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

Characterization of caulonodin lasso peptides revealed unprecedented N-terminal residues and a precursor motif essential for peptide maturation

Microbial genome mining for accelerated natural products discovery: is a renaissance in the making?

Biodiversity of genes encoding anti-microbial traits within plant associated microbes

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