Abstract
Actinobacteria are among the most prolific sources of medically and agriculturally important compounds, derived from their biosynthetic gene clusters (BGCs) for specialized (secondary) pathways of metabolism. Genomics witnesses that the majority of actinobacterial BGCs are silent, most likely due to their low or zero transcription. Much effort is put into the search for approaches towards activation of silent BGCs, as this is believed to revitalize the discovery of novel natural products. We hypothesized that the global transcriptional factor AdpA, due to its highly degenerate operator sequence, could be used to upregulate the expression of silent BGCs. Using Streptomyces cyanogenus S136 as a test case, we showed that plasmids expressing either full-length adpA or its DNA-binding domain led to significant changes in the metabolome. These were evident as changes in the accumulation of colored compounds, bioactivity, as well as the emergence of a new pattern of secondary metabolites as revealed by HPLC-ESI-mass spectrometry. We further focused on the most abundant secondary metabolite and identified it as the polyene antibiotic lucensomycin. Finally, we uncovered the entire gene cluster for lucensomycin biosynthesis (lcm), that remained elusive for five decades until now, and outlined an evidence-based scenario for its adpA-mediated activation.
Highlights
Actinobacteria are among the most prolific sources of medically and agriculturally important compounds, derived from their biosynthetic gene clusters (BGCs) for specialized pathways of metabolism
In the genome of S. cyanogenus S136, in addition to the lan cluster coding for landomycin biosynthesis, at least 33 putative BGCs were found under the default antiSMASH search conditions
In S. cyanogenus S136, the gene SCY4743 codes for a nonfunctional AdpA, and expression of heterologous adpA genes activated landomycin biosynthesis under conditions where S136 normally does not produce this antibiotic[36]
Summary
Actinobacteria are among the most prolific sources of medically and agriculturally important compounds, derived from their biosynthetic gene clusters (BGCs) for specialized (secondary) pathways of metabolism. We hypothesized that the global transcriptional factor AdpA, due to its highly degenerate operator sequence, could be used to upregulate the expression of silent BGCs. Using Streptomyces cyanogenus S136 as a test case, we showed that plasmids expressing either full-length adpA or its DNA-binding domain led to significant changes in the metabolome. As antibiotic production in streptomycetes is tightly intertwined with morphogenesis, global regulators that coordinate both aforementioned processes can be useful tools for activation of silent BGCs for known or cryptic biosynthetic pathways[27,28,29,30,31,32] Such an approach could be especially useful for activation of the BGCs lacking cluster-situated regulatory genes. AdpA-binding sites are common in silent BGCs and overexpression of adpA genes could be used for high-throughput activation of such BGCs in strains of unknown genomic background
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