Lysobacter niastensis belongs to a group of bacterial predators that produce a number of bioactive small molecules endowed with lytic properties toward other microorganisms. Here, we report the draft genome sequence of the type strain DSM 18481 and the identification of gene clusters implicated in the biosynthesis of secondary metabolites

Artuso I.

Frangipani E.

Lugli G. A.

Tescari M.

Turrini P.

Ventura M.

Visca P.

English

Archivio istituzionale della Ricerca -  Università degli Studi di Parma

11 October 2022University of Parma Research RepositoryDraft genome sequence and secondary metabolite biosynthetic potential of the lysobacter niastensis typestrain DSM 18481 / Turrini, P.; Artuso, I.; Tescari, M.; Lugli, G. A.; Frangipani, E.; Ventura, M.; Visca, P.. - In:MICROBIOLOGY RESOURCE ANNOUNCEMENTS. - ISSN 2576-098X. - 10:1(2021). [10.1128/MRA.01296-20]OriginalDraft genome sequence and secondary metabolite biosynthetic potential of the lysobacter niastensis typestrain DSM 18481Publisher:PublishedDOI:10.1128/MRA.01296-20Terms of use:openAccessPublisher copyright(Article begins on next page)Anyone can freely access the full text of works made available as "Open Access". Works made availableAvailability:This version is available at: 11381/2888544 since: 2021-02-16T18:04:16ZAmerican Society for MicrobiologyThis is the peer reviewd version of the followng article:Draft Genome Sequence and Secondary Metabolite BiosyntheticPotential of the Lysobacter niastensis Type Strain DSM 18481Paolo Turrini,a Irene Artuso,a Marco Tescari,a Gabriele Andrea Lugli,b Emanuela Frangipani,c Marco Ventura,a Paolo ViscaaaDepartment of Science, Roma Tre University, Rome, ItalybLaboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, ItalycDepartment of Biomolecular Sciences, University of Urbino Carlo Bo, Urbino, ItalyPaolo Turrini and Irene Artuso contributed equally to this work, and the order of these authors was determined on the basis of seniority.ABSTRACT Lysobacter niastensis belongs to a group of bacterial predators that pro-duce a number of bioactive small molecules endowed with lytic properties toward othermicroorganisms. Here, we report the draft genome sequence of the type strain DSM18481 and the identification of gene clusters implicated in the biosynthesis of secondarymetabolites.L ysobacter niastensis is an aerobic, rod-shaped, gliding gammaproteobacteriumbelonging to the Lysobacteraceae family (1, 2). The type strain DSM 18481 of L. nias-tensis was isolated from greenhouse soil in the Republic of Korea (2). Lysobacter speciesare bacterial predators endowed with the ability to produce lytic enzymes and pep-tides capable of causing the death of prokaryotic and eukaryotic microorganisms (3).Despite the limited genetic information available on the genus Lysobacter, some strainsare emerging sources for novel antibiotics and are amenable for biosynthetic engineer-ing (4, 5). Here, the genome of L. niastensis DSM 18481T was sequenced and analyzedfor the presence of biosynthetic gene clusters (BGCs) encoding secondary metabolites.L. niastensis DSM 18481T was obtained from the DSMZ and aerobically grown at28°C in Reasoner’s 2A (R2A) medium. DNA extraction was performed using a QIAampDNA minikit (Qiagen). A genomic library of L. niastensis was obtained with the TruSeqDNA PCR-free sample preparation kit (Illumina, Inc., San Diego, CA, USA). Genomesequencing was performed with a NextSeq 500 sequencing system, according to thesupplier’s protocol (Illumina, UK), and library samples were loaded into a midoutput kitv2.5 (300 cycles) (Illumina, UK), producing 1,670,224 paired-end reads. The rawsequence reads were filtered and trimmed using the command-line fastq-mcf software(https://expressionanalysis.github.io/ea-utils/). Fastq files of Illumina paired-end reads(150 bp) were used as input in the MEGAnnotator pipeline for microbial genome as-sembly and annotation (6). This pipeline employed the program SPAdes v3.14.0 for denovo assembly of the genome sequence with the option “--careful” and a list of k-mersizes of 21, 33, 55, 77, 99, and 127 (7). The genome quality was evaluated with the pro-gram CheckM (8), estimating a genome completeness of 99.89% and 0.86% contamina-tion. The contigs were then submitted to the National Center for BiotechnologyInformation (NCBI) for the prediction of protein-encoding open reading frames (ORFs)and tRNA and rRNA genes using the NCBI Prokaryotic Genome Annotation Pipeline(PGAP) (9). All tools were run with default parameters unless otherwise specified.The draft genome sequence of L. niastensis is 4,034,846bp long. It was assembled into15 contigs with an N50 value of 390,805bp, an average coverage of 117, and a mean GCcontent of 66.88%. Genome annotation identified 3,723 ORFs, 49 tRNA genes, and 3 rRNAgenes.The presence of six BGCs encoding putative secondary metabolites was predictedCitation Turrini P, Artuso I, Tescari M, Lugli GA,Frangipani E, Ventura M, Visca P. 2021. Draftgenome sequence and secondary metabolitebiosynthetic potential of the Lysobacterniastensis type strain DSM 18481. MicrobiolResour Announc 10:e01296-20. https://doi.org/10.1128/MRA.01296-20.Editor J. Cameron Thrash, University ofSouthern CaliforniaCopyright © 2021 Turrini et al. This is an open-access article distributed under the terms ofthe Creative Commons Attribution 4.0International license.Address correspondence to Paolo Visca,paolo.visca@uniroma3.it.Received 13 November 2020Accepted 15 December 2020Published 7 January 2021January 2021 Volume 10 Issue 1 e01296-20 mra.asm.org 1GENOME SEQUENCES on February 16, 2021 at BIBLIOTECA GENERALEhttp://mra.asm.org/Downloaded from TABLE1antiSMASHpredictedBGCsencodingsecondarymetabolitesintheLysobacterniastensisDSM18481TdraftgenomesequenceContigno.Nucleotidestart–stopposition(relativetocontigsequence)TypeaClosestknowncluster(s)(%similarity)MIBiGaccessionno.bClosesthomologofcorebiosyntheticgene(s)cSpeciesofclosesthomologIdentity(%)2161495–203387ResorcinolEicosapentaenoicacid(10)BGC00008653-oxoacyl-ACPsynthaseHalieasp.63.432438274–481902ArylpolyeneArylpolyene,APEVf(50)BGC0000837Beta-ketoacyl-ACPsynthaseLysobacterruishenii91.24Beta-ketoacyl-ACPsynthasePseudoxanthomonassp.strainPXM0474.36512052–19947BacteriocinNDdNDDUF692familyproteinLysobacterpanacisoli76.21563268–117003NRPS/T1PKSNDNDNRPSLysobactersp.strainCW23966.92T1PKSLysobactersp.strainCW23961.616254882–297695NRPS-likeNDNDAMP-bindingproteinVulcaniibacteriumgelatinicum67.047135058–145921BacteriocinNDNDDUF692domain-containingproteinLysobactercapsici78.95aThetypewasdefinedbyantiSMASHanalysis;NRPS,nonribosomalpeptidesynthetase;T1PKS,type1polyketidesynthase.bMIBiG,MinimumInformationaboutaBiosyntheticGenecluster(11);theMIBiGaccessionnumberreferstotheclosestknowncluster.cThecorebiosyntheticgenewasdefinedbyantiSMASHanalysis,andtheclosedhomologwasidentifiedbyBLASTpinterrogationoftheNCBIproteindatabaseusingL.niastensisDSM18481Tcorebiosyntheticgene(s)asquery.ACP,acylcarrierprotein.dND,notdetermined.Turrini et al.January 2021 Volume 10 Issue 1 e01296-20 mra.asm.org 2 on February 16, 2021 at BIBLIOTECA GENERALEhttp://mra.asm.org/Downloaded from using the program antiSMASH v5.1.2 (10) (Table 1). Two BGCs were involved in the bio-synthesis of putative fatty acids (eicosapentaenoic acid and an arylpolyene), twoencoded putative bacteriocins, one was predicted as a hybrid system composed of anonribosomal peptide synthetase (NRPS) and a type I polyketide synthase (T1PKS), andone was predicted as an NRPS-like cluster. Interestingly, 4 out of 6 BGCs showed no sig-nificant similarity with BGCs involved in the synthesis of known compounds, suggest-ing that their products represent novel secondary metabolites which deserve more in-depth chemical and biosynthetic characterization.Data availability. This whole-genome shotgun project has been deposited atDDBJ/ENA/GenBank under accession number JADLZT000000000. The version describedin this paper is JADLZT000000000.1. The raw sequencing reads are available at theSequence Read Archive under accession number SRR13014585 and are associated withBioProject accession number PRJNA675736.ACKNOWLEDGMENTThis work was supported by the Excellence Departments grant (art. 1 commi 314-337 Legge 232/2016) to the Department of Science, Roma Tre University, and PRIN 2017grant (Prot. 20177J5Y3P) to P.V., both from the Italian Ministry of Education, Universityand Research (MIUR).REFERENCES1. Christensen P, Cook FD. 1978. Lysobacter, a new genus of nonfruiting, glid-ing bacteria with a high base ratio. Int J Syst Evol Microbiol 28:367–393.https://doi.org/10.1099/00207713-28-3-367.2. Weon H-Y, Kim B-Y, Kim M-K, Yoo S-H, Kwon S-W, Go S-J, Stackebrandt E.2007. Lysobacter niabensis sp. nov. and Lysobacter niastensis sp. nov., iso-lated from greenhouse soils in Korea. Int J Syst Evol Microbiol 57:548–551.https://doi.org/10.1099/ijs.0.64473-0.3. Seccareccia I, Kost C, Nett M. 2015. Quantitative analysis of Lysobacter pre-dation. Appl Environ Microbiol 81:7098–7105. https://doi.org/10.1128/AEM.01781-15.4. Xie Y, Wright S, Shen Y, Du L. 2012. Bioactive natural products from Lyso-bacter. Nat Prod Rep 29:1277–1287. https://doi.org/10.1039/c2np20064c.5. Panthee S, Hamamoto H, Paudel A, Sekimizu K. 2016. Lysobacter species:a potential source of novel antibiotics. Arch Microbiol 198:839–845.https://doi.org/10.1007/s00203-016-1278-5.6. Lugli GA, Milani C, Mancabelli L, van Sinderen D, Ventura M. 2016. MEGAnno-tator: a user-friendly pipeline for microbial genomes assembly and annotation.FEMSMicrobiol Lett 363:fnw049. https://doi.org/10.1093/femsle/fnw049.7. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, LesinVM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N,Tesler G, Alekseyev MA, Pevzner PA. 2012. SPAdes: a new genomeassembly algorithm and its applications to single-cell sequencing. 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Kautsar SA, Blin K, Shaw S, Navarro-Muñoz JC, Terlouw BR, van der HooftJJJ, van Santen JA, Tracanna V, Suarez Duran HG, Pascal Andreu V, Selem-Mojica N, Alanjary M, Robinson SL, Lund G, Epstein SC, Sisto AC,Charkoudian LK, Collemare J, Linington RG, Weber T, Medema MH. 2020.MIBiG 2.0: a repository for biosynthetic gene clusters of known function.Nucleic Acids Res 48:D454–D458. https://doi.org/10.1093/nar/gkz882.Microbiology Resource AnnouncementJanuary 2021 Volume 10 Issue 1 e01296-20 mra.asm.org 3 on February 16, 2021 at BIBLIOTECA GENERALEhttp://mra.asm.org/Downloaded from 

Draft genome sequence and secondary metabolite biosynthetic potential of the lysobacter niastensis type strain DSM 18481

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Draft genome sequence and secondary metabolite biosynthetic potential of the lysobacter niastensis type strain DSM 18481

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