Genome sequence of Streptomyces gilvigriseus MUSC 26T isolated from mangrove forest

Hooi-Leng Ser Wen-Si Tan Nurul-Syakima Ab Mutalib Wai-Fong Yin Kok-Gan Chan Bey-Hing Goh Learn-Han Lee About the authors

Abstract

Streptomycetes remain as one of the important sources for bioactive products. Isolated from the mangrove forest, Streptomyces gilvigriseus MUSC 26T was previously characterised as a novel streptomycete. The high quality draft genome of MUSC 26T contained 5,213,277 bp with G + C content of 73.0%. Through genome mining, several gene clusters associated with secondary metabolites production were revealed in the genome of MUSC 26T. These findings call for further investigations into the potential exploitation of the strain for production of pharmaceutically important compounds.

Keywords:
Genome sequence; Streptomyces gilvigriseus; Mangrove; AntiSMASH; Neuroprotective

The members of Streptomyces are of great importance for bioactive products; these organisms are capable of producing a range of structurally diverse compounds with various bioactivities including antibiotics, anti-rejection (immunosuppressant), antioxidant and anticancer.11 Berdy J. Bioactive microbial metabolites. J Antibiotics. 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. As a novel streptomycete isolated from mangrove forest, Streptomyces gilvigriseus MUSC 26T has been deposited in two culture collection centres (=MCCC 1K00252T = DSM 42140T). The methanolic extract of MUSC 26T was prepared as previously described and it has demonstrated significant neuroprotective activity against free radical-induced damage in SHSY-5Y neuronal cells (data not shown).44 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.,66 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, Zainal N, Palanisamy UD, et al. Streptomyces gilvigriseus sp. nov., a novel actinobacterium isolated from mangrove forest soil. Antonie van Leeuwenhoek. 2015;107:1369-1378. Thus, the strain MUSC 26T was selected for genome sequencing as an attempt to identify biosynthetic gene clusters associated with secondary metabolites production.

Genomic DNA extraction of MUSC 26T was carried out with MasterpureTM DNA purification kit (Epicentre, Illumina Inc., Madison, WI, USA) before 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 accessed using NanoDrop spectrophotometer (Thermo Scientific, Waltham, MA, USA) and a Qubit version 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). Construction of DNA library was performed using Nextera™ DNA Sample Preparation kit (Nextera, USA) and the library quality was validated by Bioanalyser 2100 high sensitivity DNA kit (Agilent Technologies, Palo Alto, CA) prior to performing paired-end sequencing 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 206 contigs with N50 size of 45,324 bp (Table 1). The assembled genome size of MUSC 26T contained 5,213,277 bp, with an average coverage of 40.0-fold and G + C content of 73.0%. The whole genome project of MUSC 26T was deposited at DDBJ/EMBL/GenBank under accession number MLCF00000000 and the version described in this paper is the first version (MLCF01000000).

Table 1
General features of Streptomyces gilvigriseus MUSC 26T genome.

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, et al. 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 Bioinf. 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 Gen. 2008;9:75. A total of 4337 protein-encoding genes was predicted and assigned to 363 subsystems, along with 53 tRNA and 5 rRNA genes. Among the subsystems, most of the genes were involved in carbohydrates metabolism (7.39%), followed by amino acids and derivatives metabolism (5.90%) and protein metabolism subsystems (5.81%).

The genomic potential of MUSC 26T was further explored with antibiotics & Secondary Metabolite analysis shell (antiSMASH), PRediction Informatics for Secondary Metabolomes (PRISM) and BAGEL3.1414 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.

15 Skinnider MA, Dejong CA, Rees PN, et al. Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res. 2015;43:9645-9662.

16 Skinnider MA, Johnston CW, Edgar RE, et al. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. PNAS. 2016;113:E6343-E6351.
-1717 Van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP. BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic Acids Res. 2013;41:W448-W453. The antiSMASH server detected two gene clusters associated with siderophores production; one of which showed 40% similarities to desferrioxamine B biosynthetic gene cluster. The presence of these biosynthetic gene clusters suggest possible production of compounds responsible for the neuroprotective activity. Apart from siderophores, PRISM and BAGEL3 detected two gene clusters associated with class I lantipeptide and one gene cluster associated with lasso peptide and bacteriocin, respectively. Overall, these findings highlighted the genomic potential of MUSC 26T and prompted further comprehensive studies to allow utilisation of the strain for production of pharmaceutically important compounds.

Acknowledgments

This work was supported by PVC Award Grant (Project Q7 No. PVC-ECR-2016), External Industry Grant (Biotek Abadi Vote No. GBA-808813), 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

  • 1
    Berdy J. Bioactive microbial metabolites. J Antibiotics. 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.
  • 5
    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.
  • 6
    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.
  • 7
    Ser HL, Zainal N, Palanisamy UD, et al. Streptomyces gilvigriseus sp. nov., a novel actinobacterium isolated from mangrove forest soil. Antonie van Leeuwenhoek. 2015;107:1369-1378.
  • 8
    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.
  • 9
    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.
  • 10
    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, et al. consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007;35:3100-3108.
  • 12
    Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinf. 2010;11:119.
  • 13
    Aziz RK, Bartels D, Best AA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Gen 2008;9:75.
  • 14
    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.
  • 15
    Skinnider MA, Dejong CA, Rees PN, et al. Genomes to natural products prediction informatics for secondary metabolomes (PRISM). Nucleic Acids Res. 2015;43:9645-9662.
  • 16
    Skinnider MA, Johnston CW, Edgar RE, et al. Genomic charting of ribosomally synthesized natural product chemical space facilitates targeted mining. PNAS. 2016;113:E6343-E6351.
  • 17
    Van Heel AJ, de Jong A, Montalban-Lopez M, Kok J, Kuipers OP. BAGEL3: automated identification of genes encoding bacteriocins and (non-) bactericidal posttranslationally modified peptides. Nucleic Acids Res. 2013;41:W448-W453.

Publication Dates

  • Publication in this collection
    Apr-Jun 2018

History

  • Received
    10 Feb 2017
  • Accepted
    3 Apr 2017
Sociedade Brasileira de Microbiologia USP - ICB III - Dep. de Microbiologia, Sociedade Brasileira de Microbiologia, Av. Prof. Lineu Prestes, 2415, Cidade Universitária, 05508-900 São Paulo, SP - Brasil, Ramal USP 7979, Tel. / Fax: (55 11) 3813-9647 ou 3037-7095 - São Paulo - SP - Brazil
E-mail: bjm@sbmicrobiologia.org.br