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. 2019 Jun 24;7(6):181.
doi: 10.3390/microorganisms7060181.

Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential

Katherine Gregory  1 , Laura A Salvador  2 , Shukria Akbar  3 , Barbara I Adaikpoh  4 , D Cole Stevens  5
Affiliations

Survey of Biosynthetic Gene Clusters from Sequenced Myxobacteria Reveals Unexplored Biosynthetic Potential

Katherine Gregory et al. Microorganisms. .

Abstract

Coinciding with the increase in sequenced bacteria, mining of bacterial genomes for biosynthetic gene clusters (BGCs) has become a critical component of natural product discovery. The order Myxococcales, a reputable source of biologically active secondary metabolites, spans three suborders which all include natural product producing representatives. Utilizing the BiG-SCAPE-CORASON platform to generate a sequence similarity network that contains 994 BGCs from 36 sequenced myxobacteria deposited in the antiSMASH database, a total of 843 BGCs with lower than 75% similarity scores to characterized clusters within the MIBiG database are presented. This survey provides the biosynthetic diversity of these BGCs and an assessment of the predicted chemical space yet to be discovered. Considering the mere snapshot of myxobacteria included in this analysis, these untapped BGCs exemplify the potential for natural product discovery from myxobacteria.

Keywords: biosynthetic gene clusters; myxobacteria; natural product discovery.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Figures

Figure 1
Figure 1
Sequence similarity network of 994 myxobacterial BGCs deposited in the antiSMASH database generated by BiG-SCAPE and rendered with Cytoscape [9,10,13,14,16]. All GCFs that include at least 1 BGC with sequence similarity greater than ≥75% to a characterized cluster deposited in the MIBiG repository are boxed in grey (excluding 25 geosmin BGCs) [9,14]. Totals for BGC class diversity and BGCs (including 25 geosmin BGCs identified as 22 Terpene and 3 Other clusters) with and without homology to MIBiG clusters as well as color reference provided (right).
Figure 2
Figure 2
Sequence similarity network of myxobacterial BGCs classified as Others in the antiSMASH database with predicted product type and totals (right) [9].
Figure 3
Figure 3
Secondary metabolites associated with BGCs determined to possess ≥75% sequence similarity to characterized clusters in MIBiG [17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41].
Figure 4
Figure 4
Secondary metabolites associated with known BGCs from myxobacteria with sequence similarity to BGCs included in the MIBiG dataset below the 75% similarity cutoff [42,43,44,45,46,47,48,49,50,51,52,53,54,55,56].
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