Klebsiella oxytoca is an important microorganism for nitrogen fixation and chemical production. Here, we report an annotated draft genome of K. oxytoca strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs, which provides a genetic basis for a better understanding of the physiology of this species

DeLuca

Dien

Fujii

Kurtz

Pruitt

Shin

Zerbino

Zhang

English

Bao, G.

Zhang, Y.

Du, Chenyu

Chen, Z.

Li, Y.

Cao, Z.

Ma, Y.

University of Huddersfield Repository

University of Huddersfield RepositoryBao, G., Zhang, Y., Du, Chenyu, Chen, Z., Li, Y., Cao, Z. and Ma, Y.Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical ProductionOriginal CitationBao, G., Zhang, Y., Du, Chenyu, Chen, Z., Li, Y., Cao, Z. and Ma, Y. (2013) Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production. Genome Announcements, 1 (1). e00074-12. ISSN 2169-8287 This version is available at http://eprints.hud.ac.uk/23387/The University Repository is a digital collection of the research output of theUniversity, available on Open Access. Copyright and Moral Rights for the itemson this site are retained by the individual author and/or other copyright owners.Users may access full items free of charge; copies of full text items generallycan be reproduced, displayed or performed and given to third parties in anyformat or medium for personal research or study, educational or not-for-profitpurposes without prior permission or charge, provided:• The authors, title and full bibliographic details is credited in any copy;• A hyperlink and/or URL is included for the original metadata page; and• The content is not changed in any way.For more information, including our policy and submission procedure, pleasecontact the Repository Team at: E.mailbox@hud.ac.uk.http://eprints.hud.ac.uk/Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain forNitrogen Fixation and Chemical ProductionGuanhui Bao,a,b Yanping Zhang,a Chenyu Du,e,f Zugen Chen,c,d Yin Li,a Zhu’an Cao,e Yanhe Maa,dInstitute of Microbiology, Chinese Academy of Sciences, Beijing, Chinaa; University of Chinese Academy of Sciences, Beijing, Chinab; Department of Human Genetics,School of Medicine, University of California Los Angeles, Los Angeles, California, USAc; Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin,Chinad; Department of Chemical Engineering, Tsinghua University, Beijing, Chinae; School of Biosciences, University of Nottingham, Nottingham, United KingdomfKlebsiella oxytoca is an important microorganism for nitrogen fixation and chemical production. Here, we report an annotateddraft genome of K. oxytoca strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs, which provides a ge-netic basis for a better understanding of the physiology of this species.Received 4 November 2012 Accepted 19 November 2012 Published 31 January 2013Citation Bao G, Zhang Y, Du C, Chen Z, Li Y, Cao Z, Ma Y. 2013. Genome sequence of Klebsiella oxytoca M5al, a promising strain for nitrogen fixation and chemical production.Genome Announc. 1(1):e00074-12. doi:10.1128/genomeA.00074-12.Copyright © 2013 Bao et al. This is an open-access article distributed under the terms of the Attribution 3.0 Unported Creative Commons License.Address correspondence to Yanping Zhang, zhangyp@im.ac.cn.Klebsiella oxytoca is a Gram-negative bacterium that has shownpromise in utilizing a wide variety of sugars to produce valu-able chemicals and biofuels, including ethanol (1), hydrogen (2),1,3-propanediol, and 2,3-butanediol (3). The species is also ofagricultural importance due to its function in nitrogen fixation(4). To date, two complete genomes and seven draft genomes ofK. oxytoca strains have been stored in the NCBI database, amongwhich only strain KCTC 1686 showed the capability to producechemicals (2,3-butanediol) (5). Compared with the other K. oxy-toca strains, strain M5al does not have the regular polysaccharidecapsule and is therefore more easily genetically accessed and mod-ified. Moreover, the metabolic engineering of strain M5al for theproduction of 1,3-propanediol and 2,3-butanediol has been re-ported (6). Therefore, sequencing M5al will not only enrich thegenome sequence database of K. oxytoca, but it will help to under-stand the genetic background of this useful strain. Here, we reportthe genome sequence of K. oxytoca M5al and describe the se-quence differences from the genome of strain KCTC 1686.The genome of K. oxytoca M5al was sequenced using the Solexatechnology according to Illumina’s recommendations. A total of6,199,416 reads, totaling 223,178,976 bases, were obtained, pro-viding 37 coverage. Assembly was performed using AMOScmp(7) and Velvet (8), with comparative genome and de novo assem-blies, resulting in an assembly of 282 contigs of 500 bp each. Thefinal assembly includes 114 contigs after manual curation. Thetotal size of the assembly was 5.8 Mbp, with an N50 of 94.98 Kbpand a GC content of 60%. Compared to the 841-contig draftgenome of K. oxytoca strain VJSK009, a mutant derived from thewild-type strain M5al (unpublished, http://genome.wustl.edu/genomes/view/klebsiella_oxytoca_m5al), our draft genome se-quence has a significant improvement in assembly quality.The genome sequence was annotated using the NCBI Prokary-otic Genomes Automatic Annotation Pipeline (PGAAP) (9). Thedraft genome sequence of M5al contains 5,351 genes, including5,256 predicted coding sequences (CDSs), 19 rRNA genes, and 76tRNA genes. A total of 4,450 orthologous genes between strainsM5al and KCTC 1686 (GenBank accession no. NC_016612.1)were identified using the Reciprocal Smallest Distance (RSD) al-gorithm with the default parameters (10). These comparativeanalyses revealed 806 protein-coding genes that are present instrain M5al but absent in strain KCTC 1686. Among the 806 pro-teins unique to strain M5al, 231 proteins could be mapped into theKyoto Encyclopedia of Genes and Genomes (KEGG) pathways,and most of these genes were related to purine, glyoxylate anddicarboxylate, methane, and nitrogen metabolism; this explainsthe genetic basis underpinning the function of strain M5al in ni-trogen fixation and chemical production.The genome sequence of K. oxytoca M5al serves as a basis forfurther investigation of the molecular basis of its potential in ni-trogen fixation and chemical production. Relatively detailed an-notations will reveal physiological difference among the variousmutants derived from strain M5al, which showed differing capa-bilities to produce 1,3-propanediol (6).Nucleotide sequence accession numbers. This Whole Ge-nome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. AMPJ00000000. The versiondescribed in this article is the first version, AMPJ01000000.ACKNOWLEDGMENTSThis research was supported by the National Natural Science Foundationof China (grant no. 30900012) and the Scientific Equipment R&D Pro-gram of the Chinese Academy of Sciences (grant no. YZ200941). Genomesequencing was supported by the National High Technology Program ofChina (863 Project, grant no. 2012AA022101), the Knowledge InnovationProgram of the Chinese Academy of Sciences (no. KSCX2-EW-G-14-1),and the Key Technologies R&D Program of Tianjin (no. 11ZC-ZDSY08400). Y.Z. is supported by the Knowledge Innovation Program ofthe Chinese Academy of Sciences (no. KSCX2-EW-Q-14).REFERENCES1. Dien BS, Cotta MA, Jeffries TW. 2003. Bacteria engineered for fuelethanol production: current status. Appl. Microbiol. Biotechnol. 63:258 –266.Genome AnnouncementsJanuary/February 2013 Volume 1 Issue 1 e00074-12 genomea.asm.org 12. Diz HR, Felder MS, Felder J. February 2007. Method for sustainedmicrobial production of hydrogen gas in a bioreactor using Klebsiella oxy-toca. WO patent WO/2007/032798.3. Zhang G, Yang G, Wang X, Guo Q, Li Y, Li J. 2012. Influence of blockingof 2,3-butanediol pathway on glycerol metabolism for 1,3-propanediol pro-duction by Klebsiella oxytoca. Appl. Biochem. Biotechnol. 168:116–128.4. Fujii T, Huang YD, Higashitani A, Nishimura Y, Iyama S, Hirota Y,Yoneyama T, Dixon RA. 1987. Effect of inoculation with Klebsiella oxy-toca and Enterobacter cloacae on dinitrogen fixation by rice bacteria asso-ciations. Plant Soil 103:221–226.5. Shin SH, Kim S, Kim JY, Lee S, Um Y, Oh MK, Kim YR, Lee J, YangKS. 2012. Complete genome sequence of Klebsiella oxytoca KCTC 1686,used in production of 2,3-butanediol. J. Bacteriol. 194:2371–2372.6. Du C, Zhang Y, Li Y, Cao Z. 2007. Novel redox potential-based screeningstrategy for rapid isolation of Klebsiella pneumoniae mutants with en-hanced 1,3-propanediol-producing capability. Appl. Environ. Microbiol.73:4515– 4521.7. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M, Antonescu C,Salzberg SL. 2004. Versatile and open software for comparing large ge-nomes. Genome Biol. 5:R12.8. Zerbino DR, Birney E. 2008. Velvet: algorithms for de novo short readassembly using de Bruijn graphs. Genome Res. 18:821– 829.9. Pruitt KD, Tatusova T, Klimke W, Maglott DR. 2009. NCBI referencesequences: current status, policy and new initiatives. Nucleic Acids Res.37:D32–D36.10. DeLuca TF, Cui J, Jung JY, St. Gabriel KC, Wall DP. 2012. Roundup 2.0:enabling comparative genomics for over 1800 genomes. Bioinformatics28:715–716.Bao et al.Genome Announcements2 genomea.asm.org January/February 2013 Volume 1 Issue 1 e00074-12

Bacteria engineered for fuel ethanol production: current status.

Complete genome sequence of Klebsiella oxytoca KCTC 1686, used in production of 2,3-butanediol.

Effect of inoculation with Klebsiella oxytoca and Enterobacter cloacae on dinitrogen fixation by rice bacteria associations. Plant Soil 103:221–226.

Influence of blocking of 2,3-butanediol pathway on glycerol metabolism for 1,3-propanediol production by Klebsiella oxytoca.

Method for sustained microbial production of hydrogen gas in a bioreactor using Klebsiella oxytoca. WO patent WO/2007/032798.

NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res.

Novel redox potential-based screening strategy for rapid isolation of Klebsiella pneumoniae mutants with enhanced 1,3-propanediol-producing capability.

Roundup 2.0: enabling comparative genomics for over 1800 genomes. Bioinformatics 28:715–716.

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res.

Versatile and open software for comparing large genomes. Genome Biol.

Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production

ABSTRACT
          
            Klebsiella oxytoca
            is an important microorganism for nitrogen fixation and chemical production. Here, we report an annotated draft genome of
            K. oxytoca
            strain M5al that contains 5,256 protein-coding genes and 95 structural RNAs, which provides a genetic basis for a better understanding of the physiology of this species.
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Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for Nitrogen Fixation and Chemical Production

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