We report here the whole draft genome sequence of marine isolate Photobacterium halotolerans S2753, which produces the known antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant Staphylococcus aureus strains by interacting with the quorum-sensing system

Gram, Lone

Machado, Henrique

Månsson, Maria

PubMed

Online Research Database In Technology

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Downloaded from orbit.dtu.dk on: Dec 20, 2017Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of BioactiveSecondary MetabolitesMachado, Henrique; Månsson, Maria; Gram, LonePublished in:Genome AnnouncementsLink to article, DOI:10.1128/genomeA.00535-14Publication date:2014Document VersionPublisher's PDF, also known as Version of recordLink back to DTU OrbitCitation (APA):Machado, H., Månsson, M., & Gram, L. (2014). Draft Genome Sequence of Photobacterium halotolerans S2753,Producer of Bioactive Secondary Metabolites. Genome Announcements, 2(3), [e00535-14]. DOI:10.1128/genomeA.00535-14Draft Genome Sequence of Photobacterium halotolerans S2753,Producer of Bioactive Secondary MetabolitesHenrique Machado,a,b Maria Månsson,a Lone GramaDepartment of Systems Biology, Technical University of Denmark, Kgs. Lyngby, Denmarka; Novo Nordisk Foundation Center for Biosustainability, Technical University ofDenmark, Hørsholm, DenmarkbWe report here the whole draft genome sequence of marine isolate Photobacterium halotolerans S2753, which produces theknown antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant Staphylococcus aureus strains by interacting with the quorum-sensing system.Received 21 May 2014 Accepted 27 May 2014 Published 12 June 2014CitationMachado H, Månsson M, Gram L. 2014. Draft genome sequence of Photobacterium halotolerans S2753, producer of bioactive secondary metabolites. GenomeAnnounc. 2(3):e00535-14. doi:10.1128/genomeA.00535-14.Copyright © 2014 Machado et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Henrique Machado, henma@biosustain.dtu.dk.Photobacterium halotolerans strain S2753 is a Gram-negativemarine bacterium that was isolated from a mussel during theDanish global expedition Galathea 3 (1). It is able to inhibit thegrowth of bothGram-positive andGram-negative pathogens suchas Staphylococcus aureus (human pathogen) and Vibrio anguilla-rum (fish pathogen) (1, 2). This specific strain has been shown toproduce a variety of secondary metabolites with distinct bioactiv-ities (3, 4). It produces holomycin, a known antibiotic (2), as wellas a series of ngercheumicin analogues (5) (K. Adachi, Y. Kawa-bata, H. Kasai, M. Katsuta, and Y. Shizuri, 13 September 2007,Japanese patent application JP 2007–230911A) andmost interest-ingly two novel cyclodepsipeptides named solonamide A andsolonamide B (3, 4).Antimicrobial resistance in pathogens is a serious problem de-rived both from the rapid adaptation of microorganisms to anti-microbials and the recent stagnancy in antibiotic discovery. S. au-reus is a versatile pathogen that has caused particular concernrecently due to fast antimicrobial resistance development amongboth clinical and community isolates (6–8). Therefore, therapeu-tics that do not exert a killing effect, but rather interfere withvirulence of the organism, e.g., by interfering with the quorum-sensing systems, have been studied and developed in recent years(9). P. halotolerans S2753 produces compounds capable of reduc-ing the expression of virulence in S. aureus (10). Both thengercheumicins and solonamides interfere with the Agr system ofS. aureus, with solonamideBhaving the strongest interaction (10).Also, this compound can compete with the four classes of autoin-ducing peptides (AIPs) in S. aureus, although interference withAIP class III is weak.This announcement reports the draft genome sequence ofP. halotolerans S2753, a strain producing chemical compoundswith interesting features for application in biotechnological andmedical fields.High-purity genomicDNAwas extracted by successive phenol:chloroform:isoamyl-alcohol purification steps followed by pre-cipitation with isopropanol, treatment with RNase, and final pu-rification and precipitation steps (11). Quantification was done in1% agarose gel electrophoresis using a NanoDrop spectrometer(Saveen Werner, Sweden) and Qubit 2.0 analyzer (Invitrogen,United Kingdom).The sequencing of the genomes was performed by the BeijingGenomic Institute (Shenzhen, China). Libraries of 500 bp wereused for 100-bp paired-end sequencing of genomes using Illu-mina sequencing technology on an HiSeq2000 with a minimumcoverage of 100. This generated 5.03 million reads of clean data,making a total of 462,754,934 bases. The data were assembled into82 contigs (200 bp) covering 4,533,138 bases by de novo assem-bly in CLC Genomic Workbench, version 7 (CLC Bio, Aarhus,Denmark).In order to predict clusters involved in secondary metabolitesynthesis, the reported genome was run on the analysis pipelineantiSMASH (12,13), revealing the potential of this specific strain.Besides the holomycin cluster, 11 other putative clusters encodingsecondary metabolites were identified in the P. halotolerans S2753genome.Nucleotide sequence accessionnumbers.Thiswhole-genomeshotgun project has been deposited at DDBJ/EMBL/GenBank un-der the accession no. JMIB00000000. The version described in thispaper is version JMIB01000000.ACKNOWLEDGMENTSH.M. was supported by a Ph.D. grant from the People Programme (MarieCurie Actions) of the European Union’s Seventh Framework ProgrammeFP7-People-2012-ITN under grant agreement no. 317058, “BACTORY.”The sequencing was supported by the Danish Research Council for Tech-nology and Production Science with Sapere Aude (# 116262). The presentwork was carried out as part of the Galathea 3 expedition under the aus-pices of the Danish Expedition Foundation.This is Galathea 3 contribution no. p106.REFERENCES1. Gram L, Melchiorsen J, Bruhn JB. 2010. Antibacterial activity of marineculturable bacteria collected from a global sampling of ocean surface wa-ters and surface swabs of marine organisms. Mar. Biotechnol. 12:439–451. http://dx.doi.org/10.1007/s10126-009-9233-y.Genome AnnouncementsMay/June 2014 Volume 2 Issue 3 e00535-14 genomea.asm.org 12. Wietz M, Mansson M, Gotfredsen CH, Larsen TO, Gram L. 2010.Antibacterial compounds from marine Vibrionaceae isolated on a globalexpedition. Mar. Drugs 8:2946 –2960. http://dx.doi.org/10.3390/md8122946.3. Mansson M, Gram L, Larsen TO. 2011. Production of bioactive second-ary metabolites by marine Vibrionaceae. Mar. Drugs 9:1440–1468. http://dx.doi.org/10.3390/md9091440.4. Mansson M, Nielsen A, Kjærulff L, Gotfredsen CH, Wietz M, IngmerH, Gram L, Larsen TO. 2011. Inhibition of virulence gene expression inStaphylococcus aureus by novel depsipeptides from a marine photobacte-rium. Mar. Drugs 9:2537–2552. http://dx.doi.org/10.3390/md9122537.5. Kjaerulff L, Nielsen A, Mansson M, Gram L, Larsen TO, Ingmer H,Gotfredsen CH. 2013. Identification of four new agr quorum sensing-interfering cyclodepsipeptides from a marine photobacterium. Mar.Drugs 11:5051–5062. http://dx.doi.org/10.3390/md11125051.6. Herold BC, Immergluck LC, Maranan MC, Lauderdale DS, Gaskin RE,Boyle-vavra S, Leitch CD, Daum RS. 1998. Staphylococcus aureus inchildren with no identified predisposing. Risk 279:593–598.7. Diep BA, Gill SR, Chang RF, Phan TH, Chen JH, Davidson MG, Lin F,Lin J, Carleton HA, Mongodin EF, Sensabaugh GF, Perdreau-Remington F. 2006. Complete genome sequence of USA300, an epidemicclone of community-acquired meticillin-resistant Staphylococcus aureus.Lancet 367:731–739. http://dx.doi.org/10.1016/S0140-6736(06)68231-7.8. Lowy FD. 2007. Secrets of a superbug. Nat. Med. 13:1418–1420. http://dx.doi.org/10.1038/nm1207-1418.9. ShohamM. 2011. Antivirulence agents againstMRSA. FutureMedChem.3:775–777. http://dx.doi.org/10.4155/fmc.11.43.10. Nielsen A, Månsson M, Bojer MS, Gram L, Larsen TO, Novick RP,Frees D, Frøkiær H, Ingmer H. 2014. Solonamide B inhibits quorumsensing and reduces Staphylococcus aureusmediated killing of humanneu-t rophi l s . PLoS One 9 :e84992 . h t tp : / /dx .do i .org /10 .1371/journal.pone.0084992.11. Sambrook J, Russel DW. 2001. Molecular cloning: A laboratory manual.Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.12. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P,Fischbach MA, Weber T, Takano E, Breitling R. 2011. antiSMASH:rapid identification, annotation and analysis of secondary metabolite bio-synthesis gene clusters in bacterial and fungal genome sequences. NucleicAcids Res. 39:W339–W346. http://dx.doi.org/10.1093/nar/gkr466.13. Blin K, Medema MH, Kazempour D, Fischbach MA, Breitling R,Takano E, Weber T. 2013. antiSMASH 2.0—a versatile platform forgenome mining of secondary metabolite producers. Nucleic Acids Res.41:W204–W212. http://dx.doi.org/10.1093/nar/gkt449.Machado et al.Genome Announcements2 genomea.asm.org May/June 2014 Volume 2 Issue 3 e00535-14

Draft Genome Sequence of <i>Photobacterium halotolerans</i> S2753, Producer of Bioactive Secondary Metabolites

ABSTRACT
          
            We report here the whole draft genome sequence of marine isolate
            Photobacterium halotolerans
            S2753, which produces the known antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant
            Staphylococcus aureus
            strains by interacting with the quorum-sensing system.
          </jats:p

Henrique Machado

Maria Månsson

Lone Gram

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Genome Announcements

Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites

http://dx.doi.org/10.1128/genomeA.00535-14

Draft Genome Sequence of <i>Photobacterium halotolerans</i> S2753, Producer of Bioactive Secondary Metabolites

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