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GNPS - Phylogenetic conservatism of biosynthetic gene clusters and their encoded specialized metabolites

ABSTRACT: LC-MS/MS analysis of bacterial culture extracts. 30 Salinispora strains isolated from various marine sediments grown in triplicate with supplemented A1 media and extracted with ethyl acetate.

INSTRUMENT(S): 6530 Quadrupole Time-of-Flight LC/MS (Agilent instrument model)

ORGANISM(S): Salinispora Pacifica Cnr942 (ncbitaxon:1169187) Salinispora Arenicola Cnx508 (ncbitaxon:1137257) Ncbitaxon:1408341 Salinispora Tropica Cnb-440 (ncbitaxon:369723) Ncbitaxon:1408359 Salinispora Pacifica Cny237 (ncbitaxon:1169185) Salinispora Pacifica Cnt150 (ncbitaxon:1136423) Salinispora Tropica Cns416 (ncbitaxon:1169195) Salinispora Pacifica Cnt148 (ncbitaxon:1136422) Salinispora Arenicola Cnp193 (ncbitaxon:1169170) Ncbitaxon:1408350 Salinispora Pacifica Cnt855 (ncbitaxon:1137266) Ncbitaxon:1408353 Ncbitaxon:1408352 Ncbitaxon:1408351 Salinispora Pacifica Cnt609 (ncbitaxon:1169184) Salinispora Arenicola Cnh941 (ncbitaxon:1137252) Ncbitaxon:1408357 Salinispora Pacifica Cnt084 (ncbitaxon:1136419) Ncbitaxon:1408356 Ncbitaxon:1408355 Salinispora Arenicola Cnx482 (ncbitaxon:1136426) Salinispora Pacifica Cnt045 (ncbitaxon:1169190) Ncbitaxon:1408326 Salinispora Pacifica Cnt029 (ncbitaxon:1136418) Salinispora Pacifica Cns055 (ncbitaxon:1169182) Salinispora Pacifica Cny331 (ncbitaxon:1169181) Ncbitaxon:1305843 Salinispora Pacifica Cnt569 (ncbitaxon:1137263) Salinispora Pacifica Cns996 (ncbitaxon:1169189)

SUBMITTER: Paul Jensen

PROVIDER: MSV000085890 | GNPS | Sun Aug 02 16:30:00 BST 2020

REPOSITORIES: GNPS

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Project description:Inflammatory Bowel Disease (IBD) is a term describing a collection of conditions characterised by chronic inflammatory disorder of the gastrointestinal tract involving an inappropriate immune response to commensal microorganisms in a genetically susceptible host. Four kiwifruit extracts, aqueous and ethyl acetate extracts of gold kiwifruit (Actinidia chinensis) or green kiwifruit (A. deliciosa), have previously demonstrated anti-inflammatory activity using in vitro models of IBD. This study examined whether these kiwifruit extracts had immune modulating effects in vivo against inflammatory processes known to be increased in patients with IBD. KFEs were used as a dietary intervention in Il10-/- mice (an in vivo model of IBD) and the C57BL/6J background strain in a 3 x 2 factorial design. While all Il10-/- mice developed significant colonic inflammation compared to the C57BL/6J mice, this was not affected by the inclusion of KFE in the diet. Whole genome gene and protein expression level profiling indicated that KFEs influenced immune signalling pathways and metabolic processes within the colonic tissue; however, the effects were subtle. In particular, adaptive immune pathways were reduced by three out of four kiwifruit extracts, with greater reduction seen in the C57BL/6J mice. This suggests that while immune-modulating activity was present in vivo, KFEs did not reduce inflammatory processes relevant to IBD. Experimental design. Two experiments were conducted, one using extracts from gold kiwifruit and one using extracts from green kiwifruit. Within each experiment, both Il10-/- and C57 mice were randomly divided into three diet treatment groups, to ive the following 12 treatments: 1) Gold Kiwifruit Experiment, C57BL/6J mice, Control diet (AIN-76A), 2) Gold Kiwifruit Experiment, C57BL/6J mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 3) Gold Kiwifruit Experiment, C57BL/6J mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 4) Gold Kiwifruit Experiment, Il10-/- mice, Control diet (AIN-76A), 5) Gold Kiwifruit Experiment, Il10-/- mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 6) Gold Kiwifruit Experiment, Il10-/- mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 7) Green Kiwifruit Experiment, C57BL/6J mice, Control diet (AIN-76A), 8) Green Kiwifruit Experiment, C57BL/6J mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 9) Green Kiwifruit Experiment, C57BL/6J mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) 10) Green Kiwifruit Experiment, Il10-/- mice, Control diet (AIN-76A), 11) Green Kiwifruit Experiment, Il10-/- mice, Aqueous Kiwifruit Extract Supplemented Diet (AIN-76A + 5% Aqueous KFE) 12) Green Kiwifruit Experiment, Il10-/- mice, Ethyl Acetate Kiwifruit Extract Supplemented Diet (AIN-76A + 0.11% Ethyl Acetate KFE) Six biological replicates were analysed from each treatment group, except for groups 3 and 7 where five replicates were analysed due to array quality issues with the sixth replicate. Each replicate contained mRNA from one mouse. A reference design was used, where each slide was hybridised with mRNA from one sample (green channel) and mRNA from a common reference pool (red channel).

Project description:While specialized metabolites are thought to mediate ecological interactions, the evolutionary processes driving chemical 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) among 118 strains representing all nine currently named species of the marine actinobacterial genus Salinispora. While much attention has been given to the role of horizontal gene transfer (HGT) in structuring BGC distributions, we find that vertical descent facilitates interspecies BGC diversification over evolutionary timescales. Moreover, we identified a distinct phylogenetic signal among Salinispora species at both the BGC and metabolite level, indicating that specialized metabolism represents a conserved phylogenetic trait. Using a combination of genomic analyses and liquid chromatography-high-resolution tandem mass spectrometry (LC-MS/MS) targeting nine experimentally characterized BGCs and their small molecule products, we identified gene gain/loss events, constrained interspecies recombination, and other evolutionary processes associated with vertical inheritance as major contributors to BGC diversification. These evolutionary dynamics had direct consequences for the compounds produced, as exemplified by species-level differences in salinosporamide production. Together, our results support the concept that specialized metabolites, and their cognate BGCs, can represent phylogenetically conserved functional traits with chemical diversification proceeding in species-specific patterns over evolutionary time frames. IMPORTANCE Microbial natural products are traditionally exploited for their pharmaceutical potential, yet our understanding of the evolutionary processes driving BGC evolution and compound diversification remain poorly developed. While HGT is recognized as an integral driver of BGC distributions, we find that the effects of vertical inheritance on BGC diversification had direct implications for species-level specialized metabolite production. As such, understanding the degree of genetic variation that corresponds to species delineations can enhance natural product discovery efforts. Resolving the evolutionary relationships between closely related strains and specialized metabolism can also facilitate our understanding of the ecological roles of small molecules in structuring the environmental distribution of microbes.

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GNPS - Phylogenetic conservatism of biosynthetic gene clusters and their encoded specialized metabolites

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