Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

TitleComparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality
Publication TypeJournal Article
Year of Publication2017
AuthorsAmos G.CA, Awakawa T., Tuttle R.N, Letzel A.C, Kim M.C, Kudo Y., Fenical W, Moore BS, Jensen PR
JournalProceedings of the National Academy of Sciences of the United States of America
Volume114
PaginationE11121-E11130
Date Published2017/12
Type of ArticleArticle
ISBN Number0027-8424
Accession NumberWOS:000418722400008
Keywordsbiosynthetic gene cluster; diversity; global regulator; heterologous expression; marine actinomycete salinispora; mass-spectrometry; metabolism; molecular networking; myxococcus-xanthus; Salinispora; secondary metabolism; sequence; specialized; streptomyces-coelicolor a3(2); Transcriptomics
Abstract

Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of genome mining techniques based on the premise that many are transcriptionally silent during normal laboratory cultivation. Here, we employ comparative transcriptomics to assess BGC expression among four closely related strains of marine bacteria belonging to the genus Salinispora. The results reveal that slightly more than half of the BGCs are expressed at levels that should facilitate product detection. By comparing the expression profiles of similar gene clusters in different strains, we identified regulatory genes whose inactivation appears linked to cluster silencing. The significance of these subtle differences between expressed and silent BGCs could not have been predicted a priori and was only revealed by comparative transcriptomics. Evidence for the conservation of silent clusters among a larger number of strains for which genome sequences are available suggests they may be under different regulatory control from the expressed forms or that silencing may represent an underappreciated mechanism of gene cluster evolution. Coupling gene expression and metabolomics data established a bioinformatic link between the salinipostins and their associated BGC, while genetic manipulation established the genetic basis for this series of compounds, which were previously unknown from Salinispora pacifica.

DOI10.1073/pnas.1714381115
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