Abstract
BackgroundActinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The genomes of actinomycetes revealed that these bacteria have a large number of natural product gene clusters, although many of these are difficult to tie to products in the laboratory. Large scale comparisons of these clusters are difficult to perform due to the presence of highly similar repeated domains in the most common biosynthetic machinery: polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs).ResultsWe have used comparative genomics to provide an overview of the genomic features of a set of 102 closed genomes from this important group of bacteria with a focus on natural product biosynthetic genes. We have focused on well-represented genera and determine the occurrence of gene cluster families therein. Conservation of natural product gene clusters within Mycobacterium, Streptomyces and Frankia suggest crucial roles for natural products in the biology of each genus. The abundance of natural product classes is also found to vary greatly between genera, revealing underlying patterns that are not yet understood.ConclusionsA large-scale analysis of natural product gene clusters presents a useful foundation for hypothesis formulation that is currently underutilized in the field. Such studies will be increasingly necessary to study the diversity and ecology of natural products as the number of genome sequences available continues to grow.
Highlights
Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold
To provide context for the gene cluster comparisons, we constructed a phylogenetic tree using concatenated amino acid sequences from 41 ribosomal proteins shared by all strains (Figure 1). This is tree in good agreement with the phylogeny published by Gao and Gupta using 35 conserved genes from 98 actinobacterial genomes [26], there are a couple of notable differences
The work presented in this manuscript is our first step towards a systematic framework for studying natural products, a difficult bioinformatic task especially for polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs) systems
Summary
Actinomycetes are a diverse group of medically, industrially and ecologically important bacteria, studied as much for the diseases they cause as for the cures they hold. The class Actinobacteria is the largest within the phylum Actinobacteria and contains many bacteria relevant to human health and industry (see [1] for review). These bacteria are Gram-positive with genomic GC content generally over 55%. Some of them, such as the Streptomyces, were originally mistaken for fungi, as evidenced by the name of the group (myces is derived from the Greek word for fungus) and were once considered relatives of fungi based on morphology and life cycle. Numerous other pathogens and pharmaceutical producers, as well as ecologically and industrially important taxa are found among this important microbial group
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