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. 2018 Apr 26;6(17):e00194-18. doi: 10.1128/genomeA.00194-18

Draft Genome Sequence of Paucibacter aquatile CR182T, a Strain with Antimicrobial Activity Isolated from Freshwater of Nakdong River in South Korea

Eu Jin Chung a, Gang-Guk Choi a, Young-Ho Nam a, Ahyoung Choi a,✉
PMCID: PMC5920192  PMID: 29700134

ABSTRACT

This report details a draft genome sequence of Paucibacter aquatile CR182T, isolated from river water, which contains 5,523,543 bp, has a G+C content of 66.3%, and harbors 4,544 protein-coding genes in 4 contigs. These genome data provide insights into the genetic basis of this strain’s antibacterial activity and adaptive mechanisms.

GENOME ANNOUNCEMENT

The genus Paucibacter was first proposed in 2005 (1) with the type species Paucibacter toxinivorans, which belongs to the family Comamonadaceae in the phylum Betaproteobacteria. Members of the genus Paucibacter characteristically are Gram stain negative, rod shaped, and often resistant to antibiotics or toxic compounds (1–3). Here, we report the draft genome sequence of Paucibacter aquatile CR182T, isolated from freshwater of the Nakdong River, South Korea, during a screen for bacteria with antimicrobial activity (3). Strain CR182T has been deposited in the Korean Culture Center of Microorganisms (KCCM) and the Nite Biological Resource Center (NBRC) under the accession numbers KCCM 9028 and NBRC 113032, respectively.

Genomic DNA was extracted using a genomic DNA purification kit (Promega). A 20-kb SMRTbell genome library was sequenced using the PacBio RS II single-molecule real-time (SMRT) sequencing platform at ChunLab (Seoul, South Korea). The bacterial genome was assembled de novo into four contigs, with an average genome coverage of 230.9×, using the PacBio SMRT Portal (2.3.0) and the Hierarchical Genome Assembly Process (HGAP) (4). The Prokaryotic Genome Annotation System (Prokka) pipeline was used for genome annotation (5). The data were submitted to the Rapid Annotations using Subsystem Technology (RAST) server (6) and the National Center for Biotechnology Information (NBCI) genome sequence database. We searched for potential coding sequences using the Basic Local Alignment Search Tool (BLAST) against the UniProt (7), Pfam (8), and Clusters of Orthologous Groups of proteins (COG) (9) databases. Signal peptides and transmembrane helices were predicted using SignalP 4.1 (10) and TMHMM v2.0 (11). rRNA, tRNA, and other miscellaneous features were predicted using RNAmmer v1.2 (12), tRNAscan-SE v1.21 (13), and Rfam v12.0 (14).

The draft genome sequence of P. aquatile CR182T is 5,523,543 bp, with a G+C content of 66.3%. The genome is predicted to have 4,544 coding sequences (CDSs), 72 tRNA genes, and 28 rRNA genes. We identified various antibacterial genes in the genome of P. aquatile CR182T; antiSMASH shell analysis (15) revealed that the genome harbors 9 gene clusters involved in the biosynthesis of lantipeptide, hserlactone, bacteriocin, terpene, and a nonribosomal peptide synthetase (NRPS), a kind of amychelin. Analysis using the Antibiotic Resistance Genes Database (ARDB) (16) led to the identification of several genes (marB, mecR, pbp2b, catB2, bacA, smeD, and oprM) putatively involved in antibiotic resistance, some conferring specific resistance to macrolides, methicillin, penicillin, chloramphenicol, bacitracin, fluoroquinolone, and/or aminoglycosides.

The genome sequence and analysis of P. aquatile CR182T in this study provide information to further explore and reveal the mechanisms of antimicrobial action in aquatic environments.

Accession number(s).

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number POSP00000000 (BioProject number PRJNA429314). The version described in this paper is the first version.

ACKNOWLEDGMENT

This research was supported by a grant from the Nakdonggang National Institute of Biological Resources (NNIBR), funded by the Ministry of Environment (MOE) of South Korea.

Footnotes

Citation Chung EJ, Choi G-G, Nam Y-H, Choi A. 2018. Draft genome sequence of Paucibacter aquatile CR182T, a strain with antimicrobial activity isolated from freshwater of Nakdong River in South Korea. Genome Announc 6:e00194-18. https://doi.org/10.1128/genomeA.00194-18.

REFERENCES

  • 1.Rapala J, Berg KA, Lyra C, Niemi M, Manz W, Suomalainen S, Paulin L, Jahti K. 2005. Paucibacter toxinivorans gen. nov., sp. nov., a bacterium that degrades cyclic cyanobacterial hepatotoxins microcystins and nodularin. Int J Syst Evol Microbiol 55:1563–1568. doi: 10.1099/ijs.0.63599-0. [DOI] [PubMed] [Google Scholar]
  • 2.Pheng S, Lee JJ, Eom MK, Lee KH, Kim S. 2017. Paucibacter oligotrophus sp. nov., isolated from fresh water, and emended description of the genus Paucibacter. Int J Syst Evol Microbiol 67:2231–2235. doi: 10.1099/ijsem.0.001931. [DOI] [PubMed] [Google Scholar]
  • 3.Nam YH, Choi A, Hwang JM, Yim KJ, Kim J-H, Choi G-G, Chung EJ. 2018. Paucibacter aquatile sp. nov., isolated from freshwater of the Nakdong River, Republic of Korea. Arch Microbiol in press. doi: 10.1007/s00203-018-1494-2. [DOI] [PubMed] [Google Scholar]
  • 4.Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, Clum A, Copeland A, Huddleston J, Eichler EE, Turner SW, Korlach J. 2013. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 10:563–569. doi: 10.1038/nmeth.2474. [DOI] [PubMed] [Google Scholar]
  • 5.Seemann T. 2014. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068–2069. doi: 10.1093/bioinformatics/btu153. [DOI] [PubMed] [Google Scholar]
  • 6.Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M, Meyer F, Olsen GJ, Olson R, Osterman AL, Overbeek RA, McNeil LK, Paarmann D, Paczian T, Parrello B, Pusch GD, Reich C, Stevens R, Vassieva O, Vonstein V, Wilke A, Zagnitko O. 2008. The RAST server: Rapid Annotations using Subsystems Technology. BMC Genomics 9:75. doi: 10.1186/1471-2164-9-75. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 7.Wu CH, Apweiler R, Bairoch A, Natale DA, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Mazumder R, O'Donovan C, Redaschi N, Suzek B. 2006. The Universal Protein Resource (UniProt): an expanding universe of protein information. Nucleic Acids Res 34:D187–D191. doi: 10.1093/nar/gkj161. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 8.Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, Heger A, Holm L, Sonnhammer EL, Eddy SR, Bateman A, Finn RD. 2012. The Pfam protein families database. Nucleic Acids Res 40:D290–D301. doi: 10.1093/nar/gkr1065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 9.Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumdr R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41. doi: 10.1186/1471-2105-4-41. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 10.Petersen TN, Brunak S, von Heijne G, Nielsen H. 2011. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods 8:785–786. doi: 10.1038/nmeth.1701. [DOI] [PubMed] [Google Scholar]
  • 11.Krogh A, Larsson B, Von Heijne G, Sonnhammer EL. 2001. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305:567–580. doi: 10.1006/jmbi.2000.4315. [DOI] [PubMed] [Google Scholar]
  • 12.Lagesen K, Hallin P, Rødland EA, Stærfeldt HH, Rognes T, Ussery DW. 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108. doi: 10.1093/nar/gkm160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 13.Lowe TM, Eddy SR. 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 14.Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, Bateman A. 2005. Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33:D121–D124. doi: 10.1093/nar/gki081. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 15.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 biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 39:W339–W346. doi: 10.1093/nar/gkr466. [DOI] [PMC free article] [PubMed] [Google Scholar]
  • 16.Liu B, Pop M. 2009. ARDB—antibiotic resistance genes database. Nucleic Acids Res 37:D443–D447. doi: 10.1093/nar/gkn656. [DOI] [PMC free article] [PubMed] [Google Scholar]

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