ABSTRACT
As the largest genus in Actinobacteria family, Streptomyces species have the ability to synthesize numerous compounds of diverse structures with bioactivities. Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete from mangrove forest in east coast of Peninsular Malaysia. The high quality draft genome of MUSC 149T comprises 9,165,825 bp with G + C content of 72.5%. Through bioinformatics analysis, 21 gene clusters identified in the genome were associated with the production of bioactive secondary metabolites. The presence of these biosynthetic gene clusters in MUSC 149T suggests the potential exploitation of the strain for production of medically important compounds.
Keywords:
Genome sequence; Streptomyces; Mangrove; AntiSMASH; Bioinformatics analysis
Members of Streptomyces genus have received considerable attention and sparked interest among pharmaceutical industry as they are capable of synthesizing compounds of diverse structures with bioactivities including antibiotics, anti-rejection (immunosuppressant), antioxidant and anticancer.11 Berdy J. Bioactive microbial metabolites. J Antibiot. 2005;58:1-26.
2 Solecka J, Zajko J, Postek M, Rajnisz A. Biologically active secondary metabolites from Actinomycetes. Open Life Sci. 2012;7(3):373-390.
3 Tan LTH, Ser HL, Yin WF, Chan KG, Lee LH, Goh BH. Investigation of antioxidative and anticancer potentials of Streptomyces sp. MUM256 isolated from Malaysia mangrove soil. Front Microbiol. 2015;6:1316.
4 Ser HL, Tan LTH, Palanisamy UD, et al. Streptomyces antioxidans sp. nov., a novel mangrove soil actinobacterium with antioxidative and neuroprotective potentials. Front Microbiol. 2016;7:899.-55 Ser HL, Palanisamy UD, Yin WF, Chan KG, Goh BH, Lee LH. Streptomyces malaysiense sp. nov.: a novel Malaysian mangrove soil actinobacterium with antioxidative activity and cytotoxic potential against human cancer cell lines. Sci Rep. 2016;6:24247.Streptomyces mangrovisoli MUSC 149T was previously isolated as a novel streptomycete with antioxidant potential from mangrove forest in east coast of Peninsular Malaysia66 Lee LH, Zainal N, Azman AS, et al. Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia. Sci World J. 2014;698178:1-14.,77 Ser HL, Palanisamy UD, Yin WF, et al. Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-in newly isolated Streptomyces mangrovisoli sp. nov. Front Microbiol. 2015;6:854. and the strain has been deposited at two culture collection centers (=MCCC 1K00252T = DSM 42140T). Thus, the strain MUSC 149T was selected for genome sequencing as an attempt to identify biosynthetic gene clusters associated with secondary metabolite production.
The genomic DNA of MUSC 149T was extracted with Masterpure™ DNA purification kit (Epicentre, Illumina Inc., Madison, WI, USA) followed by RNase (Qiagen, USA) treatment.88 Ser HL, Tan WS, Ab Mutalib NS, et al. Genome sequence of Streptomyces pluripotens MUSC 135T exhibiting antibacterial and antioxidant activity. Mar Gen. 2015;24:281-283.,99 Ser HL, Tan WS, Ab Mutalib NS, et al. Draft genome sequence of mangrove-derived Streptomyces sp. MUSC 125 with antioxidant potential. Front Microbiol. 2016;7:1470. DNA quality was examined using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Subsequently, DNA library was constructed using Nextera™ DNA Sample Preparation kit (Nextera, USA) and the library quality was validated by Bioanalyzer 2100 high sensitivity DNA kit (Agilent Technologies, Palo Alto, CA) before performing paired-end on MiSeq platform with MiSeq Reagent Kit 2 (2× 250 bp; Illumina Inc., Madison, WI, USA). The paired-end reads were trimmed and de novo assembled with CLC Genomics Workbench version 7 (CLC bio, Denmark). The analysis generated 199 contigs with N50 size of 108,867 bp (Table 1). The assembled genome size of MUSC 149T contained 9,165,825 bp, with an average coverage of 119.0-fold and G+C content of 72.5%. The whole genome project of MUSC 149T was deposited at DDBJ/EMBL/GenBank under accession number LAVA00000000 and the version described in this paper is the second version (LAVA02000000).
Gene prediction was performed using Prodigal version 2.6, whereas rRNA and tRNA were predicted using RNAmmer and tRNAscan SE version 1.21.1010 Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955-964.
11 Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007;35:3100-3108.-1212 Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:119. The assembly was uploaded for annotation to Rapid Annotation using Subsystem Technology (RAST).1313 Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75. A total of 7461 protein-encoding genes was predicted and assigned to 442 subsystems, along with 69 tRNA and 6 rRNA genes (Fig. 1). Among the subsystems, most of the genes were involved in amino acids and derivatives metabolism (8.97%), followed by carbohydrates metabolism (8.40%) and cofactors, vitamins, prosthetic groups, pigments metabolism subsystems (4.91%).
Subsystem category distribution of Streptomyces mangrovisoli MUSC 149T (based on RAST annotation server).
In order to investigate its bioactive potential, the genome of MUSC 149T was further analyzed using antibiotics & Secondary Metabolite analysis shell (antiSMASH) version 3.0.1414 Weber T, Blin K, Duddela S, et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res. 2015;43:W237-W243. The antiSMASH server revealed 21 gene clusters related to antibiotics and secondary metabolite biosynthesis, with four clusters showed more than 70% similarities to known 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 siderophores biosynthetic gene clusters such as desferrioxamine B has further highlight the antioxidant potential of strain MUSC 149T.
In conclusion, we report the draft genome sequence of S. mangrovisoli MUSC 149T. The availability of its genome sequence has revealed production of potentially medically useful compounds and certainly deserves further detailed study.
Acknowledgments
This work was supported by PVC Award Grant (Project No. PVC-ECR-2016), External Industry Grant (Biotek Abadi Vote No. GBA-808813), Fundamental Research Grant Scheme (FRGS/1/2013/SKK01/MUSM/03/3), MOSTI eScience funds (Project No. 06-02-10-SF0300) awarded to L.-H.L. and MOSTI eScience funds (Project No. 02-02-10-SF0215) awarded to B.-H.G., and a University of Malaya for High Impact Research Grant (UM-MOHE HIR Nature Microbiome Grant No. H-50001-A000027 and No. A000001-50001) and PPP Grant (PG090-2015B) awarded to K.-G.C.
References
-
1Berdy J. Bioactive microbial metabolites. J Antibiot 2005;58:1-26.
-
2Solecka J, Zajko J, Postek M, Rajnisz A. Biologically active secondary metabolites from Actinomycetes. Open Life Sci 2012;7(3):373-390.
-
3Tan LTH, Ser HL, Yin WF, Chan KG, Lee LH, Goh BH. Investigation of antioxidative and anticancer potentials of Streptomyces sp. MUM256 isolated from Malaysia mangrove soil. Front Microbiol 2015;6:1316.
-
4Ser HL, Tan LTH, Palanisamy UD, et al. Streptomyces antioxidans sp. nov., a novel mangrove soil actinobacterium with antioxidative and neuroprotective potentials. Front Microbiol 2016;7:899.
-
5Ser HL, Palanisamy UD, Yin WF, Chan KG, Goh BH, Lee LH. Streptomyces malaysiense sp. nov.: a novel Malaysian mangrove soil actinobacterium with antioxidative activity and cytotoxic potential against human cancer cell lines. Sci Rep 2016;6:24247.
-
6Lee LH, Zainal N, Azman AS, et al. Diversity and antimicrobial activities of actinobacteria isolated from tropical mangrove sediments in Malaysia. Sci World J 2014;698178:1-14.
-
7Ser HL, Palanisamy UD, Yin WF, et al. Presence of antioxidative agent, Pyrrolo[1,2-a]pyrazine-1,4-dione,hexahydro-in newly isolated Streptomyces mangrovisoli sp. nov. Front Microbiol 2015;6:854.
-
8Ser HL, Tan WS, Ab Mutalib NS, et al. Genome sequence of Streptomyces pluripotens MUSC 135T exhibiting antibacterial and antioxidant activity. Mar Gen 2015;24:281-283.
-
9Ser HL, Tan WS, Ab Mutalib NS, et al. Draft genome sequence of mangrove-derived Streptomyces sp. MUSC 125 with antioxidant potential. Front Microbiol 2016;7:1470.
-
10Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997;25:955-964.
-
11Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100-3108.
-
12Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010;11:119.
-
13Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008;9:75.
-
14Weber T, Blin K, Duddela S, et al. antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters. Nucleic Acids Res 2015;43:W237-W243.
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Publication Dates
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Publication in this collection
Jan-Mar 2018
History
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Received
22 Dec 2016 -
Accepted
31 Jan 2017