Genome mining reveals unlocked bioactive potential of marine Gram-negative bacteria

Abstract

Background: Antibiotic resistance in bacteria spreads quickly, overtaking the pace at which new compounds are discovered and this emphasizes the immediate need to discover new compounds for control of infectious diseases. Terrestrial bacteria have for decades been investigated as a source of bioactive compounds leading to successful applications in pharmaceutical and biotech industries. Marine bacteria have so far not been exploited to the same extent; however, they are believed to harbor a multitude of novel bioactive chemistry. To explore this potential, genomes of 21 marine Alpha-and Gammaproteobacteria collected during the Galathea 3 expedition were sequenced and mined for natural product encoding gene clusters. Results: Independently of genome size, bacteria of all tested genera carried a large number of clusters encoding different potential bioactivities, especially within the Vibrionaceae and Pseudoalteromonadaceae families. A very high potential was identified in pigmented pseudoalteromonads with up to 20 clusters in a single strain, mostly NRPSs and NRPS-PKS hybrids. Furthermore, regulatory elements in bioactivity-related pathways including chitin metabolism, quorum sensing and iron scavenging systems were investigated both in silico and in vitro. Genes with siderophore function were identified in 50% of the strains, however, all but one harboured the ferric-uptake-regulator gene. Genes encoding the syntethase of acylated homoserine lactones were found in Roseobacter-clade bacteria, but not in the Vibrionaceae strains and only in one Pseudoalteromonas strains. The understanding and manipulation of these elements can help in the discovery and production of new compounds never identified under regular laboratory cultivation conditions. High chitinolytic potential was demonstrated and verified for Vibrio and Pseudoalteromonas species that commonly live in close association with eukaryotic organisms in the environment. Chitin regulation by the ChiS histidine-kinase seems to be a general trait of the Vibrionaceae family, however it is absent in the Pseudomonadaceae. Hence, the degree to which chitin influences secondary metabolism in marine bacteria is not known.

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

“…Two of our R. mobilis strains were isolated from copepods, however, chitinases were not detected in the genomes. Instead, we identified the complete uptake system for N-acetylglucosamine dimers including the sensor chiS (Li and Roseman, 2004;Machado et al, 2015). This could present an example of R. mobilis not only being a supplier of nutrients, but also benefiting from the leaky production by others.…”

Biological Potential of Chitinolytic Marine Bacteria

“…The bacterial genomes have previously been mined for chitinase genes and ChiS [28], and we here extend this genome mining including also COD, LPMO and a subdivision of the chitinase genes (Table 1). Two to six putative chitinase genes were found in the 10 chitin degrading strains, and all but one strain, V. galatheae S2757, also encoded one to two putative LPMOs.…”

“…The bacteria were isolated during the Galathea 3 expedition [25] and they have been whole-genome sequenced [28]. Genomes were assembled using CLC Genomics Workbench 7 (CLC bio, Aarhus, Denmark) and contig-based draft genomes were obtained.…”

Influence of Niche-Specific Nutrients on Secondary Metabolism in Vibrionaceae

“…However, this potential can often not be unfolded and detected under standard laboratory conditions (3,4), and, today, one challenge in the discovery of natural products is to elicit these silent/cryptic biosynthetic gene clusters. The one strain-many compounds method, where strains are cultivated under a range of growth conditions, has been suggested as a solution (5).…”