Sweeney, D. | Search bioRxiv

bioRxiv2024

Pattern-based genome mining guides discovery of the antibiotic indanopyrrole A from a marine streptomycete.

Terrestrial actinomycetes in the genus Streptomyces have long been recognized as prolific producers of small molecule natural products, including many clinically important antibiotics and cytotoxic agents. Although Streptomyces can also be isolated from marine environments, their potential for natural product biosynthesis remains underexplored. The MAR4 clade of largely marine-derived Streptomyces has been a rich source of novel halogenated natural products of diverse structural classes. To further explore the biosynthetic potential of this group, we applied pattern-based genome mining leading to the discovery of the first halogenated pyrroloketoindane natural products, indanopyrrole A (1) and B (2), and the bioinformatic linkage of these compounds to an orphan biosynthetic gene cluster (BCG) in 20 MAR4 genomes. Indanopyrrole A displays potent broad-spectrum antibiotic activity against clinically relevant pathogens. A comparison of the putative indanopyrrole BGC with that of the related compound indanomycin provides new insights into the terminal cyclization and offloading mechanisms in pyrroloketoindane biosynthesis. Broader searches of public databases reveal the rarity of this BGC while also highlighting opportunities for discovering additional compounds in this uncommon class. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/620887v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@14d6080org.highwire.dtl.DTLVardef@fa89b5org.highwire.dtl.DTLVardef@66fdddorg.highwire.dtl.DTLVardef@1a4f7f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2023

Rapid and sensitive detection of genome contamination at scale with FCS-GX

Assembled genome sequences are being generated at an exponential rate. Here we present FCS-GX, part of NCBIs Foreign Contamination Screen (FCS) tool suite, optimized to identify and remove contaminant sequences in new genomes. FCS-GX screens most genomes in 0.1-10 minutes. Testing FCS-GX on artificially fragmented genomes demonstrates sensitivity >95% for diverse contaminant species and specificity >99.93%. We used FCS-GX to screen 1.6 million GenBank assemblies and identified 36.8 Gbp of contamination (0.16% of total bases), with half from 161 assemblies. We updated assemblies in NCBI RefSeq to reduce detected contamination to 0.01% of bases. FCS-GX is available at https://github.com/ncbi/fcs/.

bioinformatics↗

bioRxiv2020

Complex evolutionary dynamics govern the diversity and distribution of biosynthetic gene clusters and their encoded specialized metabolites

While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving their diversification, particularly among closely related lineages, remain poorly understood. Here, we examine the evolutionary dynamics governing the distribution of natural product biosynthetic gene clusters (BGCs) using 118 strains within the marine actinomycete genus Salinispora. While previous evidence indicated that horizontal gene transfer (HGT) largely contributed to BGC diversity, we find that a majority of BGCs in Salinispora genomes are conserved through processes of vertical descent. In particular, vertical inheritance maintained BGCs over evolutionary timescales (millions of years) allowing for BGC diversification among Salinispora species. By coupling the genomic analyses with high-resolution tandem mass spectrometry (LC-MS/MS), we identified that BGC evolution in Salinispora proceeds largely through gene gain/loss events and constrained recombination that contributes to interspecies diversity at the gene, pathway, and metabolite levels. Consequently, the evolutionary processes driving BGC diversification had direct consequences for compound production and contributed to chemical diversification, as exemplified in our case study of the medically relevant proteosome inhibitors, the salinosporamides. Together, our results support the concept that specialized metabolites, and their cognate BGCs, represent functional traits associated with niche differentiation among Salinispora species. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=107 SRC="FIGDIR/small/423547v2_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@aef190org.highwire.dtl.DTLVardef@17536baorg.highwire.dtl.DTLVardef@5bf336org.highwire.dtl.DTLVardef@bc7d2f_HPS_FORMAT_FIGEXP M_FIG C_FIG O_TEXTBOXSIGNIFICANCENatural products are traditionally exploited for their pharmaceutical potential; yet what is often overlooked is that the evolution of the biosynthetic gene clusters (BGCs) encoding these small molecules likely affects the diversification of the produced compounds and implicitly has an impact on the compounds activities and ecological functions. And while the prevailing dogma in natural product research attributes frequent and widespread horizontal gene transfer (HGT) as an integral driver of BGC evolution, we find that the majority of BGC diversity derives from processes of vertical descent, with HGT events being rare. This understanding can facilitate informed biosynthetic predictions to identify novel natural products, in addition to uncovering how these specialized metabolites contribute to the environmental distribution of microbes. C_TEXTBOX

microbiology↗