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

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by  Bao, Guanhui

Genome Sequence of Klebsiella oxytoca M5al, a Promising Strain for
Nitrogen Fixation and Chemical Production
GuanhuiBao,a,bYanpingZhang,aChenyuDu,e,fZugenChen,c,dYinLi,aZhu’anCao,eYanheMaa,d
InstituteofMicrobiology,ChineseAcademyofSciences,Beijing,Chinaa;UniversityofChineseAcademyofSciences,Beijing,Chinab;DepartmentofHumanGenetics,
SchoolofMedicine,UniversityofCaliforniaLosAngeles,LosAngeles,California,USAc;TianjinInstituteofIndustrialBiotechnology,ChineseAcademyofSciences,Tianjin,
Chinad;DepartmentofChemicalEngineering,TsinghuaUniversity,Beijing,Chinae;SchoolofBiosciences,UniversityofNottingham,Nottingham,UnitedKingdomf
Klebsiellaoxytocaisanimportantmicroorganismfornitrogenfixationandchemicalproduction.Here,wereportanannotated
draftgenomeofK.oxytocastrainM5althatcontains5,256protein-codinggenesand95structuralRNAs,whichprovidesage-
neticbasisforabetterunderstandingofthephysiologyofthisspecies.
Received4November2012 Accepted19November2012 Published31January2013
CitationBaoG,ZhangY,DuC,ChenZ,LiY,CaoZ,MaY.2013.GenomesequenceofKlebsiellaoxytocaM5al,apromisingstrainfornitrogenfixationandchemicalproduction.
GenomeAnnounc.1(1):e00074-12.doi:10.1128/genomeA.00074-12.
Copyright©2013Baoetal.Thisisanopen-accessarticledistributedunderthetermsoftheAttribution3.0UnportedCreativeCommonsLicense.
AddresscorrespondencetoYanpingZhang,[email protected].
KlebsiellaoxytocaisaGram-negativebacteriumthathasshown M5al and KCTC 1686 (GenBank accession no. NC_016612.1)
promiseinutilizingawidevarietyofsugarstoproducevalu- wereidentifiedusingtheReciprocalSmallestDistance(RSD)al-
ablechemicalsandbiofuels,includingethanol(1),hydrogen(2), gorithm with the default parameters (10). These comparative
1,3-propanediol, and 2,3-butanediol (3). The species is also of analyses revealed 806 protein-coding genes that are present in
agricultural importance due to its function in nitrogen fixation strainM5albutabsentinstrainKCTC1686.Amongthe806pro-
(4).Todate,twocompletegenomesandsevendraftgenomesof teinsuniquetostrainM5al,231proteinscouldbemappedintothe
K.oxytocastrainshavebeenstoredintheNCBIdatabase,among Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways,
whichonlystrainKCTC1686showedthecapabilitytoproduce and most of these genes were related to purine, glyoxylate and
chemicals(2,3-butanediol)(5).ComparedwiththeotherK.oxy- dicarboxylate, methane, and nitrogen metabolism; this explains
tocastrains,strainM5aldoesnothavetheregularpolysaccharide thegeneticbasisunderpinningthefunctionofstrainM5alinni-
capsuleandisthereforemoreeasilygeneticallyaccessedandmod- trogenfixationandchemicalproduction.
ified.Moreover,themetabolicengineeringofstrainM5alforthe ThegenomesequenceofK.oxytocaM5alservesasabasisfor
production of 1,3-propanediol and 2,3-butanediol has been re- furtherinvestigationofthemolecularbasisofitspotentialinni-
ported(6).Therefore,sequencingM5alwillnotonlyenrichthe trogenfixationandchemicalproduction.Relativelydetailedan-
genomesequencedatabaseofK.oxytoca,butitwillhelptounder- notationswillrevealphysiologicaldifferenceamongthevarious
standthegeneticbackgroundofthisusefulstrain.Here,wereport mutantsderivedfromstrainM5al,whichshoweddifferingcapa-
the genome sequence of K. oxytoca M5al and describe the se- bilitiestoproduce1,3-propanediol(6).
quencedifferencesfromthegenomeofstrainKCTC1686. Nucleotide sequence accession numbers. This Whole Ge-
ThegenomeofK.oxytocaM5alwassequencedusingtheSolexa nome Shotgun project has been deposited at DDBJ/EMBL/
technologyaccordingtoIllumina’srecommendations.Atotalof GenBank under the accession no. AMPJ00000000. The version
6,199,416reads,totaling223,178,976bases,wereobtained,pro- describedinthisarticleisthefirstversion,AMPJ01000000.
viding37(cid:1)coverage.AssemblywasperformedusingAMOScmp
(7)andVelvet(8),withcomparativegenomeanddenovoassem- ACKNOWLEDGMENTS
blies,resultinginanassemblyof282contigsof(cid:2)500bpeach.The ThisresearchwassupportedbytheNationalNaturalScienceFoundation
final assembly includes 114 contigs after manual curation. The ofChina(grantno.30900012)andtheScientificEquipmentR&DPro-
totalsizeoftheassemblywas5.8Mbp,withanN of94.98Kbp gramoftheChineseAcademyofSciences(grantno.YZ200941).Genome
50
and a G(cid:3)C content of 60%. Compared to the 841-contig draft sequencingwassupportedbytheNationalHighTechnologyProgramof
genomeofK.oxytocastrainVJSK009,amutantderivedfromthe China(863Project,grantno.2012AA022101),theKnowledgeInnovation
wild-type strain M5al (unpublished, http://genome.wustl.edu ProgramoftheChineseAcademyofSciences(no.KSCX2-EW-G-14-1),
and the Key Technologies R&D Program of Tianjin (no. 11ZC-
/genomes/view/klebsiella_oxytoca_m5al), our draft genome se-
ZDSY08400).Y.Z.issupportedbytheKnowledgeInnovationProgramof
quencehasasignificantimprovementinassemblyquality.
theChineseAcademyofSciences(no.KSCX2-EW-Q-14).
ThegenomesequencewasannotatedusingtheNCBIProkary-
oticGenomesAutomaticAnnotationPipeline(PGAAP)(9).The
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