Arsukibacterium ikkense GCM72(T) and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline environments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the two draft genome sequences, which may serve as sources of future industrial enzymes

Glaring, Mikkel Andreas

Hallin, Peter F

Hansen, Lea Benedicte Skov

Jepsen, Morten

Lylloff, Jeanette Eva

Stougaard, Peter

Sørensen, Søren Johannes

English

PubMed

Copenhagen University Research Information System

u n i ve r s i t y  o f  co pe n h ag e n  Københavns UniversitetDraft genome sequences of two protease-producing strains of Arsukibacterium,isolated from two cold and alkaline environmentsLylloff, Jeanette Eva; Hansen, Lea Benedicte Skov; Jepsen, Morten; Hallin, Peter F;Sørensen, Søren Johannes; Stougaard, Peter; Glaring, Mikkel AndreasPublished in:Genome AnnouncementsDOI:10.1128/genomeA.00585-15Publication date:2015Document versionPublisher's PDF, also known as Version of recordCitation for published version (APA):Lylloff, J. E., Hansen, L. B. S., Jepsen, M., Hallin, P. F., Sørensen, S. J., Stougaard, P., & Glaring, M. A. (2015).Draft genome sequences of two protease-producing strains of Arsukibacterium, isolated from two cold andalkaline environments. Genome Announcements, 3(3), [e00585-15]. https://doi.org/10.1128/genomeA.00585-15Download date: 03. Feb. 2020Draft Genome Sequences of Two Protease-Producing Strains ofArsukibacterium, Isolated from Two Cold and Alkaline EnvironmentsJeanette E. Lylloff,a Lea B. S. Hansen,b* Morten Jepsen,a Peter F. Hallin,c Søren J. Sørensen,b Peter Stougaard,a Mikkel A. GlaringaDepartment of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmarka; Department of Biology, University of Copenhagen, Copenhagen,Denmarkb; Novozymes A/S, Bagsværd, Denmarkc* Present address: Lea B. S. Hansen, Technical University of Denmark DTU, Lyngby, Denmark.Arsukibacterium ikkenseGCM72T and a close relative, Arsukibacterium sp. MJ3, were isolated from two cold and alkaline envi-ronments as producers of extracellular proteolytic enzymes active at high pH and low temperature. This report describes the twodraft genome sequences, which may serve as sources of future industrial enzymes.Received 29 April 2015 Accepted 5 May 2015 Published 4 June 2015Citation Lylloff JE, Hansen LBS, Jepsen M, Hallin PF, Sørensen SJ, Stougaard P, Glaring MA. 2015. Draft genome sequences of two protease-producing strains ofArsukibacterium, isolated from two cold and alkaline environments. Genome Announc 3(3):e00585-15. doi:10.1128/genomeA.00585-15.Copyright © 2015 Lylloff et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 3.0 Unported license.Address correspondence to Peter Stougaard, psg@plen.ku.dk.Cold and alkaline environments are very rare on Earth, andknowledge regarding the organisms that thrive in such poly-extreme environments is limited. The submarine ikaite tufa col-umns in the Ikka Fjord in southwest Greenland represent aunique, permanently cold (6°C), and alkaline (pH 10) envi-ronment (1) and have been shown to harbor a diverse bacterialcommunity adapted to these conditions (2–4). A large number ofbacteria from the ikaite columns have previously been isolated,and many of these produce extracellular enzymes active at highpH and low temperature (5, 6). One isolate producing high levelsof extracellular proteolytic activity was characterized asArsukibac-terium ikkense GCM72T (7). A close protease-producing relative(98.6% identity between 16S rRNA genes) was isolated from aseries of alkaline ponds located in the McMurdo Dry Valley regionin the Antarctica and named Arsukibacterium sp. MJ3. Bothstrains grow optimally at 15°C and pH 9 to 10 and produce extra-cellular proteolytic enzymes active at 5°C and pH 10. In this re-port, we describe the annotated draft genome sequences of thesetwo strains of Arsukibacterium. The genome sequences are part ofan ongoing research effort aimed at identifying new cold- andalkaline-active hydrolytic enzymes.Genomic DNA was isolated from liquid cultures growing instandard R2 broth medium supplemented with 1% NaCl. Ge-nome sequences were obtained by Illumina HiSeq paired-end se-quencing of a short insert library. Assembly was performed usingCLC Genomics Workbench (http://www.clcbio.com) for A. ik-kense, resulting in a 4,127,744-bp genome assembly in 44 contigs(400 bp) with an N50 contig length of 187,051 bp, and usingIDBA (8) for Arsukibacterium sp. MJ3, resulting in a 3,746,433-bpassembly in 196 contigs (400 bp) with an N50 contig length of146,257 bp. The GC content was 48.55%, and 46.02% for A. ik-kense and Arsukibacterium sp. MJ3, respectively. Annotation ofthe genomes through the NCBI Prokaryotic Genome AnnotationPipeline resulted in 3,605 predicted coding sequences and 63 RNAsequences in the A. ikkense genome and 3,330 predicted codingsequences and 67 RNA sequences in the Arsukibacterium sp. MJ3genome. The closest characterized relative of both strains isRheinheimera perlucida type strain BA124 (DSM 15883), isolatedfrom the Baltic Sea (9).The genomes of both strains encode a number of putative ex-tracellular proteases, including several serine proteases of the sub-tilisin type and numerous oligo-, di-, and exopeptidases, whichmay function in complete degradation of extracellular protein fornutritional purposes. Preliminary exoproteomic data on A. ik-kense indicate that many of these proteases are secreted to thegrowth medium and may thus be responsible for the observedproteolytic activity at low temperature and high pH.Nucleotide sequence accessionnumbers.This whole-genomeshotgun project has been deposited in DDBJ/ENA/GenBank un-der the accession numbers LAHO00000000 (A. ikkense GCM72)and LAHP00000000 (Arsukibacterium sp. MJ3). The versions de-scribed in this paper are the first versions, LAHO01000000 andLAHP01000000.ACKNOWLEDGMENTSThis work was supported by a grant from the Danish EnvironmentalProtection Agency to P.S. and by the Danish Council for Strategic Re-search (project NOVENIA).REFERENCES1. Buchardt B, Seaman P, Stockmann G, Vous M, Wilken U, Düwel L,Kristiansen A, Jenner C, Whiticar MJ, Kristensen RM, Petersen GH,Thorbjørn L. 1997. Submarine columns of ikaite tufa. Nature 390:129 –130. http://dx.doi.org/10.1038/36474.2. Glaring MA, Vester JK, Lylloff JE, Abu Al-Soud W, Sørensen SJ, Stou-gaard P. 2015. Microbial diversity in a permanently cold and alkaline en-vironment in Greenland. PLoS One 10:e0124863. http://dx.doi.org/10.1371/journal.pone.0124863.3. Schmidt M, Priemé A, Stougaard P. 2006. Bacterial diversity in perma-nently cold and alkaline ikaite columns from Greenland. Extremophiles10:551–562. http://dx.doi.org/10.1007/s00792-006-0529-9.4. Vester JK, Glaring MA, Stougaard P. 2013. Improving diversity in culturesof bacteria from an extreme environment. Can J Microbiol 59:581–586.http://dx.doi.org/10.1139/cjm-2013-0087.5. Vester JK, Glaring MA, Stougaard P. 2014. Discovery of novel enzymescrossmarkGenome AnnouncementsMay/June 2015 Volume 3 Issue 3 e00585-15 genomea.asm.org 1 on June 25, 2015 by KB, Københavns Universitetsbibliotekhttp://genomea.asm.org/Downloaded from with industrial potential from a cold and alkaline environment by a com-bination of functional metagenomics and culturing. Microb Cell Fact 13:72. http://dx.doi.org/10.1186/1475-2859-13-72.6. Vester JK, Glaring MA, Stougaard P. 2015. An exceptionally cold-adaptedalpha-amylase from a metagenomic library of a cold and alkaline environ-ment. Appl Microbiol Biotechnol 99:717–727. http://dx.doi.org/10.1007/s00253-014-5931-0.7. Schmidt M, Priemé A, Stougaard P. 2007. Arsukibacterium ikkense gen.nov., sp. nov., a novel alkaliphilic, enzyme-producing gamma-proteobacterium isolated from a cold and alkaline environment in Green-land. Syst Appl Microbiol 30:197–201. http://dx.doi.org/10.1016/ j.sy-apm.2006.05.003.8. Peng Y, Leung HCM, Yiu SM, Chin FYL. 2012. IDBA-UD: a de novoassembler for single-cell and metagenomic sequencing data with highlyuneven depth. Bioinformatics 28:1420 –1428. http://dx.doi.org/10.1093/bioinformatics/bts174.9. Brettar I, Christen R, Höfle MG. 2006. Rheinheimera perlucida sp. nov., amarine bacterium of the Gammaproteobacteria isolated from surface waterof the central Baltic sea. Int J Syst Evol Microbiol 56:2177–2183. http://dx.doi.org/10.1099/ijs.0.64172-0.Lylloff et al.Genome Announcements2 genomea.asm.org May/June 2015 Volume 3 Issue 3 e00585-15 on June 25, 2015 by KB, Københavns Universitetsbibliotekhttp://genomea.asm.org/Downloaded from 

Draft genome sequences of two protease-producing strains of <i>Arsukibacterium</i>, isolated from two cold and alkaline environments

http://dx.doi.org/10.1128/genomeA.00585-15

Draft genome sequences of two protease-producing strains of <i>Arsukibacterium</i>, isolated from two cold and alkaline environments

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