Complete genome sequence of a phthalic acid esters degrading Mycobacterium sp. YC-RL4

brazilian journal of microbiology48(2017)607–609

h tt p : / / w w w . b j m i c r o b i o l . c o m . b r /

Genome

Announcements

Complete

genome

sequence

of

a

phthalic

acid

esters

degrading

Mycobacterium

sp.

YC-RL4

Lei

Ren

_,

_Shuanghu

_Fan

_,

_Junhuan

_Wang,

_Nahurira

_Ruth,

_Cheng

_Qiao,

_Yang

_Jia,

Yanchun

Yan

ChineseAcademyofAgriculturalSciences,GraduateSchool,No.12ZhongguancunSouthStreet,Beijing,China

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Articlehistory:

Received29May2016

Accepted14September2016

Availableonline3June2017

AssociateEditor:JohnMcCulloch

Keywords:

GenomeSequence

Mycobacteriumsp. Biodegradation

Phthalicacidesters

a

b

s

t

r

a

c

t

Mycobacteriumsp.YC-RL4iscapableofutilizingabroadrangeofphthalicacidesters(PAEs)

assolesourceofcarbonandenergyforgrowth.Thepreliminarystudiesdemonstratedits

highdegradingefficiencyandgoodperformanceduringthebioprocesswithenvironmental

samples.Here,wepresentthecompletegenomeofMycobacteriumsp.YC-RL4,which

con-sistsofonecircularchromosome(5,801,417bp)andoneplasmid(252,568bp).Thegenomic

analysisandgeneannotationwereperformedandmanypotentialgenesresponsiblefor

thebiodegradationofPAEswereidentifiedfromthegenome.Theseresultsmayadvance

theinvestigationofbioremediationofPAEs-contaminatedenvironmentsbystrainYC-RL4.

©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.Thisis

anopenaccessarticleundertheCCBY-NC-NDlicense(http://creativecommons.org/

licenses/by-nc-nd/4.0/).

Plasticizershavebeenusedasadditivesinplasticorpolymeric

materialstoimprovetheirflexibility,transparency,durability,

and longevity.PAEsare amongthe mostwidelyused

plas-ticizers.These PAEsdonot physicallybind to the polymer

matrixofproductsandcaneasilymigratetotheenvironment.

ThedetectionofPAEsinsoil,water,andairhasbeenwidely

reported.ThetoxicityevaluationofPAEsindicatedtheir

devel-opmentalandreproductivetoxicitytohumanandanimals.1,2

PAEsarelistedastop-priorityenvironmentalpollutantsbythe

UnitedStatesEnvironmentProtectionAgency(USEPA)andthe

EuropeanUnion.3_{Greateffortshavebeenmadetoeliminate}

PAEsfromtheenvironmentandbiodegradationisamongthe

mostwidelyinvestigatedmethods.

∗ _{Correspondingauthor.Tel.:+861082109685;fax:+861082106609.}

E-mail:yanyanchun@caas.cn(Y.Yan).

1 _{Theseauthorsequallycontributedtothisworkandshouldbeconsideredasco-firstauthor.}

VariousPAEs-degradingbacteriahaveisolatedand

charac-terized,includinggeneraGordonia,Pseudomonas,Burkholderia,

andBacillus.4–8_{AlthoughPAEs-degradingisolatesand}

degrad-ingpathwaywerewidelyreported,theknowledgeofdegrading

relatedmolecularmechanismislimited. Previously,we

iso-latedMycobacteriumsp.YC-RL4frompetroleumcontaminated

soil, which was capable of utilizing several kinds of PAEs

as sole sourceofcarbon and energyforgrowth.9 _Here,we

reportthe completegenome sequenceofMycobacteriumsp.

YC-RL4andwehopethegenomicinformationwouldadvance

ourunderstandingofPAEsdegradingmechanism,whichmay

providenewgeneresourcesforbiotechnologyandgene

engi-neering.

http://dx.doi.org/10.1016/j.bjm.2016.09.022

1517-8382/©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.ThisisanopenaccessarticleundertheCC

608

Table1–GeneralgenomefeaturesofMycobacteriumsp. YC-RL4.

Features Chromosome pMYC1

Length(bp) 5,801,417 252,568

G+Ccontent(%) 67.48 65.7

Totalnumberofgenes 5532 249

Proteincodinggenes 5385 249

tRNAs 47 0

rRNAgenes 6 0

ThegenomicDNA ofstrain YC-RL4wasextractedusing theBacterialGenomicDNAExtractionkit(Takara,Japan),and thequalityandquantitywereevaluatedbyBioanalyzer2100 (Agilent)beforesequencing.ThegenomeofstrainYC-RL4was sequencedusingSingleMolecular,Real-Time(SMRT) technol-ogywiththe PacBioRSII platform.Afterqualitycontrol, a totallengthof1,550,468,925bpdatawasobtainedwith 256-foldaveragecoverage.Allreadsweredenovoassembledusing MHAP(v8.0).10,11 _{Theassembled genomewasannotated by}

NCBIProkaryoticGenomeAnnotationPipeline.12_Protein

cod-ingsequences,tRNAandrRNAwereidentified.

ThegeneratedgenomesequencesrevealedstrainYC-RL4

comprises6,053,985bp,whichwerefinallyassembledintoone

circularchromosome(5,801,417bp)withanaverageG+C

con-tentof67.48%andoneplasmid(pMYC01,252,568bp)witha

averageG+Ccontentof65.7%.Intotal,5781geneswere

pre-dicted,including5634proteincoding sequences,47 tRNAs,

and6rRNAgenes.Allthegenomicinformationandannotated

resultswerepresentedinTable1.

Microorganisms can evolve different strategies to fit

theenvironment.Weanalyzedthepotentialbiodegradation

related genes. Several genes and gene clusters located in

thegenomeandplasmidthatmay contributetothe

degra-dationofPAEswere identified. Thebiodegradation ofPAEs

wasalwaysinitialedbyhydrolyzingoftwoesterbonds(Ren

et al., 2016).The generated phthalic acid (PA) was further

utilizedbyringcleavage. Oneesterasegeneinthegenome

sequence responsible for the hydrolyzation of monoalkyl

phthalates(MAPs)toPA(MAPswastheintermediateofPAEs

catabolism)wasidentified.13,14Inaddition,completebenzoate

metabolismpathwaywasidentifiedand locatedingenome

sequence,whichmay beinvolvedinthemetabolismofPA.

Some aromatic compounds catabolism related genes were

alsoannotatedinthegenome.Meanwhile,annotationof

path-waywas performed byassigning predicted genes toKyoto

EncyclopediaofGenesandGenomes(KEGG)database15_and

2206CDSswereinvolvedin117pathways.Thegenome

infor-mationofstrainYC-RL4wouldbeusefulforelucidatingthe

molecularmechanismofPAEsmetabolismandprovidesnew

approachforthebioremediationofPAEscontaminated

envi-ronments.

Strain

and

nucleotide

sequence

accession

numbers

ThisstrainhasbeendepositedinChinaGeneral

Microbiologi-calCultureCollectionCenter(CGMCC)withdepositnumberas

CGMCCNo.10993.Thechromosomeandplasmidsequences

ofMycobacteriumsp.YC-RL4weredepositedinGenBankunder

theaccessionnumbersCP015596andCP015597,respectively.

Conflicts

of

interest

Theauthorsdeclarenoconflictsofinterest.

Acknowledgements

This work was supported bythe National Natural Science

FoundationofChina(31540067,31170119),andBasicResearch

FundofCAAS(0042014006,0042012003and0042011006).

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