258 lines
18 KiB
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258 lines
18 KiB
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@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
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@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
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@prefix bibo: <http://purl.org/ontology/bibo/> .
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@prefix cito: <http://purl.org/spar/cito/> .
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@prefix dc: <http://purl.org/dc/elements/1.1/> .
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@prefix dwc: <http://rs.tdwg.org/dwc/terms/> .
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@prefix dwcFP: <http://filteredpush.org/ontologies/oa/dwcFP#> .
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@prefix fabio: <http://purl.org/spar/fabio/> .
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@prefix trt: <http://plazi.org/vocab/treatment#> .
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<http://treatment.plazi.org/id/40239D056F769B45FCF71CAB8C43C83F>
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# Warning: Not adding 'trt:citesTaxonName <http://taxon-name.plazi.org/id/Animalia/the>' due to issues with rank, Not adding 'trt:citesTaxonName <http://taxon-name.plazi.org/id/Animalia/through>' due to issues with rank ;
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cito:cites <http://dx.doi.org/10.5281/zenodo.8235153>, <http://dx.doi.org/10.5281/zenodo.8235155>, <http://dx.doi.org/10.5281/zenodo.8235157>, <http://dx.doi.org/10.5281/zenodo.8235159>, <http://dx.doi.org/10.5281/zenodo.8235161>, <http://taxon-concept.plazi.org/id/Bacteria/Bacillales_Prevot_1953>, <http://taxon-concept.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens_Mtcc_>, <http://taxon-concept.plazi.org/id/Bacteria/Enterococcus_feacalis_Andrewes_1906>, <http://taxon-concept.plazi.org/id/Bacteria/Enterococcus_tarda_Mtcc_2400>, <http://taxon-concept.plazi.org/id/Bacteria/Klebsiella_pneumoniae_Schroeter_1886>, <http://taxon-concept.plazi.org/id/Bacteria/Pseudomonas_aeruginosa_Schroeter_1872>, <http://taxon-concept.plazi.org/id/Bacteria/Staphylococcus_aureus_Vre_>, <http://taxon-concept.plazi.org/id/Bacteria/Streptococcus_pyogenes_Mtcc_1924> ;
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dc:creator "Chakraborty, Kajal; Kizhakkekalam, Vinaya Kizhakkepatt; Joy, Minju" ;
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dc:title "Bacillus amyloliquefaciens L. M. Liao 1987" ;
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trt:augmentsTaxonConcept <http://taxon-concept.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens_Fukumoto_1943> ;
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trt:citesTaxonName <http://taxon-name.plazi.org/id/Bacteria/Bacillus>, <http://taxon-name.plazi.org/id/Bacteria/Bacillus_undetermined>, <http://taxon-name.plazi.org/id/Bacteria/Brevibacillus_undetermined>, <http://taxon-name.plazi.org/id/Bacteria/Enterococcus_coli>, <http://taxon-name.plazi.org/id/Bacteria/Vibrio_parahaemolyticus>, <http://taxon-name.plazi.org/id/Plantae/Arabidopsis_thaliana>, <http://taxon-name.plazi.org/id/Plantae/Kappaphycus_alvarezii> ;
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trt:publishedIn <http://dx.doi.org/10.1016/j.phytochem.2021.112983> ;
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a trt:Treatment .
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<http://dx.doi.org/10.1016/j.phytochem.2021.112983>
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bibo:endPage "13" ;
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bibo:journal "Phytochemistry" ;
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bibo:pubDate "2022-01-31" ;
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bibo:series "112983" ;
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bibo:startPage "1" ;
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bibo:volume "193" ;
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dc:creator "Chakraborty, Kajal; Kizhakkekalam, Vinaya Kizhakkepatt; Joy, Minju" ;
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dc:date "2022" ;
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dc:title "Polyketide-derived macrobrevins from marine macroalga-associated Bacillus amyloliquefaciens as promising antibacterial agents against pathogens causing nosocomial infections" ;
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fabio:hasPart <http://dx.doi.org/10.5281/zenodo.8235153>, <http://dx.doi.org/10.5281/zenodo.8235155>, <http://dx.doi.org/10.5281/zenodo.8235157>, <http://dx.doi.org/10.5281/zenodo.8235159>, <http://dx.doi.org/10.5281/zenodo.8235161> ;
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a fabio:JournalArticle .
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<http://taxon-concept.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens_Fukumoto_1943>
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dwc:ID-ENA "1390" ;
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dwc:authority "Priest et al., 1987" ;
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dwc:authorityName "L. M. Liao" ;
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dwc:authorityYear "1987" ;
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dwc:baseAuthorityName "ex. Fukumoto" ;
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dwc:baseAuthorityYear "1943" ;
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dwc:class "Bacilli" ;
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dwc:family "Bacillaceae" ;
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dwc:genus "Bacillus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(ex. Fukumoto, 1943) Liao, 1987" ;
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dwc:species "amyloliquefaciens" ;
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rdfs:seeAlso <https://www.catalogueoflife.org/data/taxon/K8MZ> ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens_Mtcc_>
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dwc:authority "MTCC" ;
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dwc:authorityName "MTCC" ;
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dwc:class "Bacilli" ;
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dwc:family "Bacillaceae" ;
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dwc:genus "Bacillus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "Mtcc" ;
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dwc:species "amyloliquefaciens" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Bacillales_Prevot_1953>
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dwc:authorityName "Prevot" ;
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dwc:authorityYear "1953" ;
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dwc:class "Bacilli" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "order" ;
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dwc:scientificNameAuthorship "Prevot, 1953" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Bacillales> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Pseudomonas_aeruginosa_Schroeter_1872>
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dwc:authorityName "Migula" ;
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dwc:authorityYear "1900" ;
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dwc:baseAuthorityName "Schroeter" ;
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dwc:baseAuthorityYear "1872" ;
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dwc:class "Betaproteobacteria" ;
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dwc:family "Burkholderiaceae" ;
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dwc:genus "Pseudomonas" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Burkholderiales" ;
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dwc:phylum "Proteobacteria" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(Schroeter, 1872) Migula, 1900" ;
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dwc:species "aeruginosa" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Pseudomonas_aeruginosa> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Klebsiella_pneumoniae_Schroeter_1886>
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dwc:authorityName "Trevisan" ;
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dwc:authorityYear "1887" ;
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dwc:baseAuthorityName "Schroeter" ;
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dwc:baseAuthorityYear "1886" ;
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dwc:class "Gammaproteobacteria" ;
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dwc:family "Enterobacteriaceae" ;
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dwc:genus "Klebsiella" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Enterobacteriales" ;
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dwc:phylum "Proteobacteria" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(Schroeter, 1886) Trevisan, 1887" ;
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dwc:species "pneumoniae" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Klebsiella_pneumoniae> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Enterococcus_tarda_Mtcc_2400>
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dwc:authority "(MTCC 2400)" ;
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dwc:baseAuthorityName "MTCC" ;
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dwc:baseAuthorityYear "2400" ;
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dwc:class "Bacilli" ;
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dwc:family "Enterococcaceae" ;
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dwc:genus "Enterococcus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Lactobacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(Mtcc, 2400)" ;
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dwc:species "tarda" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Enterococcus_tarda> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Streptococcus_pyogenes_Mtcc_1924>
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dwc:authority "(MTCC, 1924)" ;
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dwc:baseAuthorityName "MTCC" ;
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dwc:baseAuthorityYear "1924" ;
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dwc:class "Bacilli" ;
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dwc:family "Streptococcaceae" ;
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dwc:genus "Streptococcus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Lactobacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(Mtcc, 1924)" ;
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dwc:species "pyogenes" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Streptococcus_pyogenes> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Staphylococcus_aureus_Vre_>
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dwc:authority ", VRE" ;
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dwc:authorityName "VRE" ;
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dwc:class "Bacilli" ;
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dwc:family "Staphylococcaceae" ;
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dwc:genus "Staphylococcus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "Vre" ;
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dwc:species "aureus" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Staphylococcus_aureus> ;
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a dwcFP:TaxonConcept .
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<http://taxon-concept.plazi.org/id/Bacteria/Enterococcus_feacalis_Andrewes_1906>
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dwc:authorityName "Schleifer & Kilpper-Bälz" ;
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dwc:authorityYear "1984" ;
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dwc:baseAuthorityName "Andrewes & Horder" ;
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dwc:baseAuthorityYear "1906" ;
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dwc:class "Bacilli" ;
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dwc:family "Enterococcaceae" ;
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dwc:genus "Enterococcus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Lactobacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:scientificNameAuthorship "(Andrewes & Horder, 1906) Schleifer & Kilpper-Bälz, 1984" ;
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dwc:species "feacalis" ;
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trt:hasTaxonName <http://taxon-name.plazi.org/id/Bacteria/Enterococcus_feacalis> ;
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a dwcFP:TaxonConcept .
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<http://taxon-name.plazi.org/id/Bacteria/Bacillus_amyloliquefaciens>
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dwc:class "Bacilli" ;
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dwc:family "Bacillaceae" ;
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dwc:genus "Bacillus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "species" ;
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dwc:species "amyloliquefaciens" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria/Bacillus> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria/Bacillus>
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dwc:class "Bacilli" ;
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dwc:family "Bacillaceae" ;
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dwc:genus "Bacillus" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "genus" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria/Bacillaceae> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria/Bacillaceae>
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dwc:family "Bacillaceae" ;
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dwc:rank "family" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria/Bacillales> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria/Bacillales>
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dwc:class "Bacilli" ;
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dwc:kingdom "Bacteria" ;
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dwc:order "Bacillales" ;
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dwc:phylum "Firmicutes" ;
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dwc:rank "order" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria/Bacilli> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria/Bacilli>
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dwc:class "Bacilli" ;
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dwc:rank "class" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria/Firmicutes> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria/Firmicutes>
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dwc:phylum "Firmicutes" ;
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dwc:rank "phylum" ;
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trt:hasParentName <http://taxon-name.plazi.org/id/Bacteria> ;
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a dwcFP:TaxonName .
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<http://taxon-name.plazi.org/id/Bacteria>
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dwc:kingdom "Bacteria" ;
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dwc:rank "kingdom" ;
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a dwcFP:TaxonName .
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<http://dx.doi.org/10.5281/zenodo.8235153>
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dc:description "Fig. 1. Structural representation of (A) trihydroxy-decahydro-37-methyl-macrobrevin (compound 1), (B) hexahydro-macrobrevin (compound 2), (C) hexahydro-41- hydroxy-macrobrevin-31-acetate (compound 3), and (D) hexahydro-28-nor-methyl-5-methoxy-macrobrevin (compound 4) isolated from marine macroalgaassociated B. amyloliquefaciens MTCC 12713. (E) The zone of inhibition (34 mm) observed with hexahydro-41-hydroxy-macrobrevin-31-acetate (compound 3) against VREfs as visualized on Mueller Hinton agar plates by disc diffusion assay was illustrated. The amounts of compound 3 and chloramphenicol were 30 μg per disc. Chloramphenicol and ethyl acetate, which were used as the positive and negative control, were denoted with (+) and (), respectively." ;
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fabio:hasRepresentation <https://zenodo.org/record/8235153/files/figure.png> ;
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a fabio:Figure .
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<http://dx.doi.org/10.5281/zenodo.8235155>
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dc:description "Fig. 2. 1H–1H COSY/HMBC (A-D) correlations of macrobrevin analogues (1–4). Key 1H–1H COSY correlations and HMBC pairings were characterized by bold-faced bonds and double-barbed arrows, respectively." ;
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fabio:hasRepresentation <https://zenodo.org/record/8235155/files/figure.png> ;
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a fabio:Figure .
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<http://dx.doi.org/10.5281/zenodo.8235157>
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dc:description "Fig. 3. (A) Biosynthetic gene cluster coding for biosynthesis of macrobrevin analogues in B. amyloliquefaciens showing 46% similarity with macrobrevin biosynthetic gene cluster BGC0001470 (as elucidated by Known-Cluster-Blast prediction, the gene cluster also had 32% similarity with aurantinine and bacillaene with 100% similarity), (B) organization of genes in macrobrevin biosynthetic gene cluster of Brevibacillus sp. (C) Domain organization of the modules of trans-AT PKS gene cluster coding for bacillaene, which is 46% similar to macrobrevin biosynthetic gene cluster is shown. (D) The proposed functions of genes (1–16) contained in the biosynthetic gene cluster has been listed out, and are described as: (1) Biosynthetic additional (smcogs) SMCOG1170: metallo-β-lactamase family protein (score: 203; E-value: 5.4e-62); (2) biosynthetic trans-AT-PKS:PKS_AT biosynthetic additional SMCOG1021: malonyl CoA-acyl carrier protein transacylase (score: 400.8; E-value: 1.8e-121); (3) biosynthetic trans AT-PKS:PKS_AT biosynthetic additional SMCOG1021: malonyl CoA-acyl carrier protein transacylase (score: 232.8; E-value: 1.5e-70); (4) biosynthetic trans-AT-PKS:PKS_AT biosynthetic additional SMCOG1021:malonyl CoA-acyl carrier protein transacylase (score: 481.1; E-value: 9e-146); (5) biosynthetic additional PP-binding; (6) biosynthetic T3PKS:Chal_sti_synt_N biosynthetic additional SMCOG1043:hydroxymethylglutaryl-CoA synthase (score: 496.9; E-value: 6.5e-151); (7) biosynthetic additional SMCOG1023: enoyl-CoA hydratase (score: 228.4; E-value: 1.3e-69); (8) biosynthetic trans-AT-PKS:PP-binding biosynthetic trans-AT-PKS:tra_KS-biosynthetic trans AT-PKS:ATd-biosynthetic NRPS:AMP-binding biosynthetic-NRPS: condensation biosynthetic additional adh_short biosynthetic additional SMCOG1127: condensation domain-containing protein (score: 295.3; E-value: 1.6e-89); (9) biosynthetic additional-tra_KS biosyntheticadditional SMCOG1022: β-ketoacyl synthase (score: 160.9; E-value: 8.3e-49); (10) biosynthetic-trans-AT-PKS:PP-binding-biosynthetic-trans-AT-PKS:tra_KS-biosynthetic-trans-AT-KS:ATd-biosynthetic-additional-adh_short-biosynthetic-additional-SMCOG1001:short-chain-dehydrogenase/reductase SDR (score: 48.7; E-value: 1.2e-14); (11) biosynthetic-trans-AT-PKS:PP-binding-biosynthetic-trans-AT-PKS:tra_KS-biosynthetic-trans-AT-PKS:ATd-biosynthetic-additional-adh_short-biosynthetic-additional SMCOG1093: β-ketoacyl synthase (score: 73.2; E-value: 2.8e-22); (12) biosynthetic trans AT-PKS: PP-binding-biosynthetic-trans-AT-PKS:tra_KSbiosynthetic-trans-AT-PKS:ATd-biosynthetic-additional-adh biosynthetic-additional SMCOG1022: β-ketoacyl synthase (score: 222.6; E-value: 1.5e-67); (13) biosynthetic-additional-condensation biosynthetic-additional SMCOG1127:condensation domain-containing protein (score: 196.8; E-value: 1.3e-59); (14) biosynthetic-trans-AT-PKS:PP-binding-biosynthetic-trans-AT-PKS:tra_KS-biosynthetic-trans-AT-PKS:ATd-biosynthetic-NRPS-like:AMP-binding-biosynthetic-NRPS-like:PPbinding-biosynthetic-additional adh_short-biosynthetic-additional SMCOG1002: AMP-dependent synthetase and ligase (score: 373.7; E-value: 1.9e-113); (15) biosynthetic-additional-PP-binding-biosynthetic-additional-tra_KS-biosynthetic-additional MCOG1022: β-ketoacyl (score: 73.2; E-value: 2.8e-22); (16) biosynthetictrans-AT-PKS-like:tra_KS-biosynthetic-trans-AT-PKS-like:ATd-biosynthetic-additional-PP-binding-biosynthetic-additional SMCOG1022: β-ketoacyl synthase (score: 207.7; E-value: 5.1e-63)." ;
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fabio:hasRepresentation <https://zenodo.org/record/8235157/files/figure.png> ;
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a fabio:Figure .
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<http://dx.doi.org/10.5281/zenodo.8235159>
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dc:description "Fig. 4. Proposed biosynthesis of 21- membered macrocyclic lactones classified as macrobrevin analogues (1–4) in B. amyloliquefaciens through successive decarboxylative Claisen condensation between acetyl-S-KS domain and malonate-S- ACP units. Claisen condensation was activated by acyl carrier protein (ACP), ketoreductase (KR), ketosynthase (KS), thioesterase (TE), dehydratase (DH), methyl transferase (MT), acyl transferase (AT), enoyl reductase (ER) and S-adenosyl-methionine (SAM). The elongation process comprised of 16 modules with KS, KR and ACP domains. The initial step includes the decarboxylative Claisen condensation between 2-methylbutanethioic-S-KS and malonate-S-ACP. The final step of macrobrevin formation could occur through the cyclization of linear chain of 21-membered carbon framework by TE. Consequently, alterations of 21-membered carbon framework classified as macrobrevin scaffold could result in the formation of macrobrevin analogues 1–4." ;
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fabio:hasRepresentation <https://zenodo.org/record/8235159/files/figure.png> ;
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a fabio:Figure .
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<http://dx.doi.org/10.5281/zenodo.8235161>
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dc:description "Fig. 5. (A) Molecular docking interfaces of 41-hydroxy-macrobrevin-31-acetate (compound 3) with S. aureus peptide deformylase (SaPDF). 3D docking analysis of the titled macrobrevin analogue (ligand) and S. aureus PDF crystal structure (PDB ID: 1LQW) were conformationally structured (Swiss-Pdb Viewer, SPDBV, version 4.1.0). The primary algorithm used by AutoDock for conformational searching was the Lamarckian Genetic Algorithm (LGA) showing four hydrogen bonds each (displayed as red and bluecoloured lines) in the binding site, whereas USCF Chimera (University of California, San Francisco, ver. 1.11.2) software reinforced the visualizations of the best molecular docking positions of the compound and target protein. The contact residues were shown and labeled by type and number in the background. Compound 3 exhibited least binding energy among the titled compounds. (B) Illustrative representation of 41-hydroxy-macrobrevin-31-acetate (compound 3) forming hydrogen bond interactions with the amino acyl residues in the active site of SaPDF. Compound (3) displayed maximum number of hydrogen bond interactions (GLN141 at 3.118 Å, LYS84 at 3.789 Å and 3.388 Å, and ARG143 at 3.483 Å). (C) Drug-likeness score obtained for the compound (3) with molsoft software. (For interpretation of the references to color in this figure legend, the reader is referred to the Web version of this article.)" ;
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