Genome sequence of Streptomyces mangrovisoli MUSC 149T isolated from intertidal sediments

brazilian journal of microbiology 49(2018)13–15

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

Genome

Announcement

Genome

sequence

of

Streptomyces

mangrovisoli

MUSC

149

T

isolated

from

intertidal

sediments

Hooi-Leng

Ser

_,

_Wen-Si

_Tan

_,

_{Nurul-Syakima}

_Ab

_Mutalib

_,

_Wai-Fong

_Yin

_,

Kok-Gan

Chan

_,

_Bey-Hing

_Goh

_,

_Learn-Han

_Lee

a_{MonashUniversityMalaysia,SchoolofPharmacy,NovelBacteriaandDrugDiscovery(NBDD)ResearchGroup,SelangorDarulEhsan,}

Malaysia

b_{MonashUniversityMalaysia,JeffreyCheahSchoolofMedicineandHealthSciences,BiomedicalResearchLaboratory,SelangorDarul}

Ehsan,Malaysia

c_{UniversityofMalaya,InstituteofBiologicalSciences,DivisionofGeneticsandMolecularBiology,KualaLumpur,Malaysia}

d_{UniversityKebangsaanMalaysia,UKMMedicalCentre,UKMMedicalMolecularBiologyInstitute(UMBI),KualaLumpur,Malaysia}

e_{UniversityofPhayao,SchoolofPharmaceuticalSciences,CenterofHealthOutcomesResearchandTherapeuticSafety(Cohorts),}

Phayao,Thailand

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Articlehistory:

Received22December2016

Accepted31January2017

Availableonline6September2017

AssociateEditor:JohnMcCulloch

Keywords: Genomesequence Streptomyces Mangrove AntiSMASH Bioinformaticsanalysis

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AsthelargestgenusinActinobacteriafamily,Streptomycesspecieshavetheabilityto

synthe-sizenumerouscompoundsofdiversestructureswithbioactivities.Streptomycesmangrovisoli

MUSC 149T _{was previouslyisolated asa novel streptomycetefrommangrove forestin}

eastcoastofPeninsularMalaysia.ThehighqualitydraftgenomeofMUSC149T_comprises

9,165,825bpwithG+Ccontent of72.5%.Throughbioinformaticsanalysis,21gene

clus-tersidentifiedinthegenomewereassociatedwiththeproductionofbioactivesecondary

metabolites.ThepresenceofthesebiosyntheticgeneclustersinMUSC149T_suggeststhe

potentialexploitationofthestrainforproductionofmedicallyimportantcompounds.

©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.Thisis

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

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

Members of Streptomyces genus have received

consider-able attention and sparked interest among

pharmaceu-tical industry as they are capable of synthesizing

com-pounds of diverse structures with bioactivities including

antibiotics,anti-rejection(immunosuppressant),antioxidant

and anticancer.1–5 _{Streptomyces mangrovisoli MUSC 149}T

was previously isolated as a novel streptomycete with

∗ _{Correspondingauthorat:SchoolofPharmacy,MonashUniversityMalaysia,47500BandarSunway,SelangorDarulEhsan,Malaysia.}

E-mails:lee.learn.han@monash.edu,leelearnhan@yahoo.com(L.Lee).

antioxidantpotentialfrommangroveforestineastcoastof

Peninsular Malaysia6,7 _{and the strain has been deposited}

at two culture collection centers (=MCCC 1K00252T_=DSM

42140T_{). Thus, the strain MUSC 149}T _{was selected for}

genome sequencing as an attempt to identify

biosyn-thetic gene clusters associated with secondary metabolite

production.

https://doi.org/10.1016/j.bjm.2017.01.013

1517-8382/©2017SociedadeBrasileiradeMicrobiologia.PublishedbyElsevierEditoraLtda.ThisisanopenaccessarticleundertheCC

14

Table1–GeneralfeaturesofStreptomycesmangrovisoli

MUSC149T_genome. Streptomycesmangrovisoli MUSC149T Genomesize(bp) 9,165,825 Contigs 199 ContigsN50(bp) 108,867 G+Ccontent% 72.5

Proteincodinggenes 7461

tRNA 69

rRNA 4(5S),1(16S),1(23S)

The genomic DNA of MUSC 149T _{was extracted with} MasterpureTM _{DNA purification kit (Epicentre, Illumina} Inc., Madison, WI, USA) followed by RNase (Qiagen, USA) treatment.8,9 _{DNA quality was examined using NanoDrop}

spectrophotometer (ThermoScientific, Waltham, MA, USA)

andaQubitversion2.0fluorometer(LifeTechnologies,

Carls-bad, CA, USA). Subsequently,DNA library was constructed

usingNexteraTM_{DNASamplePreparationkit(Nextera,USA)}

and the library quality was validated by Bioanalyzer 2100

highsensitivityDNAkit(AgilentTechnologies,PaloAlto,CA)

beforeperformingpaired-endonMiSeqplatformwithMiSeq

ReagentKit2(2× 250bp; IlluminaInc.,Madison,WI,USA).

Thepaired-endreadsweretrimmedanddenovoassembled

withCLCGenomicsWorkbenchversion7(CLCbio,Denmark).

Theanalysisgenerated199contigswithN50sizeof108,867bp

(Table1).TheassembledgenomesizeofMUSC149T_contained

9,165,825bp,withanaveragecoverageof119.0-foldandG+C

content of72.5%.ThewholegenomeprojectofMUSC149T

wasdepositedatDDBJ/EMBL/GenBankunderaccession

num-berLAVA00000000andtheversiondescribedinthispaperis

thesecondversion(LAVA02000000).

GenepredictionwasperformedusingProdigalversion2.6,

whereasrRNAandtRNAwerepredictedusingRNAmmerand

tRNAscanSEversion1.21.10–12_{Theassemblywasuploadedfor}

annotationtoRapidAnnotationusingSubsystemTechnology

(RAST).13_{Atotalof7461protein-encodinggeneswaspredicted}

and assignedto442subsystems, alongwith69 tRNAand6

rRNAgenes(Fig.1).Amongthesubsystems,mostofthegenes

were involved in amino acids and derivatives metabolism

(8.97%), followed by carbohydrates metabolism(8.40%) and

cofactors,vitamins,prostheticgroups,pigmentsmetabolism

subsystems(4.91%).

Inordertoinvestigateitsbioactivepotential,thegenome

ofMUSC149T_{wasfurtheranalyzedusingantibiotics&}

Sec-ondary Metaboliteanalysisshell (antiSMASH)version3.0.14

The antiSMASH server revealed 21 gene clusters related

to antibiotics and secondary metabolite biosynthesis, with

four clusters showedmorethan 70% similarities toknown

gene clusters: venezuelin biosynthetic gene cluster (75%),

ectoine biosynthetic gene cluster (75%), desferrioxamine B

biosynthetic gene cluster (83%), and hopene biosynthetic

gene cluster (85%). Previously, extract of MUSC 149T _was

found to possess antioxidant activity; the presence of

siderophoresbiosyntheticgeneclusterssuchas

desferrioxam-ineBhasfurtherhighlighttheantioxidantpotentialofstrain

MUSC149T_.

In conclusion, we report the draft genome sequence of

S. mangrovisoli MUSC 149T_{. The availability of its genome}

sequence has revealed production ofpotentially medically

useful compounds and certainly deserves further detailed

study.

Subsystem coverage Subsystem category distribution Subsystem feature counts

Cofactors, vitamins, prosthetic groups, pigments (392) cell wall and capsule (162)

Virulence, disease and defense (74) Photosynthesis (0)

Miscellaneous (75)

Phages, prophages,transposable elements,plasmids (6) Potassium metabolism (22)

Membrance transport (106) Iron acquisition and metabolism (36) RNA metabolism (126)

Nucleosides and nucleotides (139) Protein metabolism (335) Cell division and cell cycle (34) Motility and chemotaxis (6) Regulation and cell signaling (64) Secondary metabolism (9) DNA metabolism (128)

Fatty acids, lipids, and isoprenoids (315) Nitrogen metabolism (44)

Dormancy and sporulation (11) Respiration (167)

Stress response (186)

Metabolism of aromatic compounds (113) Amino acids and derivatives (717) Sulfur metabolism (76) Phosphorus metabolism (47) Carbohydrates (671)

32%

68%

brazilian journal of microbiology49(2018)13–15

15

Conflicts

of

interest

Theauthorsdeclarenoconflictsofinterest.

Acknowledgments

Thiswork wassupported byPVCAward Grant(Project No.

PVC-ECR-2016), External IndustryGrant (Biotek Abadi Vote

No. GBA-808813), Fundamental Research Grant Scheme

(FRGS/1/2013/SKK01/MUSM/03/3), MOSTI eScience funds

(ProjectNo.06-02-10-SF0300)awardedtoL.-H.L. andMOSTI

eScience funds (Project No. 02-02-10-SF0215) awarded to

B.-H.G.,andaUniversityofMalayaforHighImpactResearch

Grant(UM-MOHEHIRNatureMicrobiomeGrantNo.

H-50001-A000027andNo.A000001-50001)andPPPGrant(PG090-2015B)

awardedtoK.-G.C.

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