Draft genome sequence of Streptomyces sp. strain F1, a potential source for glycoside hydrolases isolated from Brazilian soil

Ricardo Rodrigues de Melo Gabriela Felix Persinoti Douglas Antonio Alvaredo Paixão Fábio Márcio Squina Roberto Ruller Helia Harumi Sato About the authors

ABSTRACT

Here, we show the draft genome sequence of Streptomyces sp. F1, a strain isolated from soil with great potential for secretion of hydrolytic enzymes used to deconstruct cellulosic biomass. The draft genome assembly of Streptomyces sp. strain F1 has 69 contigs with a total genome size of 8,142,296 bp and G + C 72.65%. Preliminary genome analysis identified 175 proteins as Carbohydrate-Active Enzymes, being 85 glycoside hydrolases organized in 33 distinct families. This draft genome information provides new insights on the key genes encoding hydrolytic enzymes involved in biomass deconstruction employed by soil bacteria.

Keywords:
Actinobacteria; Glycoside hydrolases; Streptomyces; Draft genome sequence; Soil bacteria

Introduction

Streptomyces species are aerobic Gram-positive bacteria best known industrially as producers of natural antibiotics,11 Barbe V, Bouzon M, Mangenot S, et al. Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. J Bacteriol. 2011;193(18):5055-5056. but they are also recognized for their capacity to utilize cellulosic biomass.22 Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci Rep. 2013;3:1030. Phylogenetically, Streptomyces is the largest genus of the Actinobacteria phylum. During their lifetime, these soil bacteria are able to differentiate, produce aerial mycelia and a wide variety of secondary metabolites.33 Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex extracellular biology of Streptomyces. FEMS Microbiol Rev. 2010;34(2):171-198. Although a large number of Streptomyces species can grow on plant biomass, understanding of key genes encoding hydrolytic enzymes involved in biomass degrading by Streptomyces is currently limited to a few soil-isolates.22 Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces. Sci Rep. 2013;3:1030.,44 Franco-Cirigliano MN, Rezende RDC, Gravina-Oliveira MP, et al. Streptomyces misionensis PESB-25 produces a thermoacidophilic endoglucanase using sugarcane bagasse and corn steep liquor as the sole organic substrates. Biomed Res Int. 2013;2013:1-10.

5 Wibberg D, Al-Dilaimi A, Busche T, et al. Complete genome sequence of Streptomyces reticuli, an efficient degrader of crystalline cellulose. J Biotechnol Elsevier BV. 2016;222:13-14.

6 Book AJ, Lewin GR, McDonald BR, et al. Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically linked capacity to degrade lignocellulose. Appl Environ Microbiol. 2014;80(15):4692-4701.
-77 Semêdo LTAS, Gomes RC, Linhares AA, et al. Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil. Int J Syst Evol Microbiol. 2004;54(4):1323-1328.Streptomyces sp. strain F1 was isolated from soil containing decomposing organic matter collected in Campinas, São Paulo, Brazil. This isolated strain showed ability to grow in culture medium containing cellulose or hemicellulose as sole carbon source, and to secrete extracellular enzymes belonging to the glycoside hydrolases (GHs) families. Glycoside hydrolases are a group of enzymes that play an important role in the conversion of lignocellulosic biomass into small chemical building blocks, which can then be used to produce biofuels and other important intermediary molecules.88 Horn S, Vaaje-Kolstad G, Westereng B, Eijsink VG. Novel enzymes for the degradation of cellulose. Biotechnol Biofuels. 2012;5(1):45. Here, we show the draft genome sequence of Streptomyces sp. F1, to identify GHs family members and to improve understanding of natural biomass utilization by soil bacteria.

Genomic DNA extraction from Streptomyces sp. F1 was carried out using FastDNA SPIN Kit for soil (MP Biomedicals, Irvine, CA) according to the manufacturer's instructions. The genome was sequenced by whole genome shotgun sequencing using the Illumina HiSeq 2500 System at CTBE Sequencing and Robotics NGS facility, generating 8,147,881 paired end reads (2× 100 bp). Reads were preprocessed with Trimmomatic,99 Bolger AM, Lohse M, Trimmomatic Usadel B. A flexible trimmer for Illumina Sequence Data. Bioinforma Adv. 2014;30:2114. to remove low-quality and adapter sequences and were assembled using Spades version 3.6.1010 Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-477. The genome size was estimated to be 8,205,272, with approximately 100× coverage. The draft genome assembly of Streptomyces sp. F1 has 69 contigs, 8,142,296 bp in length with G + C content of 72.65% (Table 1), an N50 of 296,926 bp, and the largest contig was 760,841 bp. Genome completeness was evaluated using CheckM,1111 Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW, Check M. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25(7):1043-1055. which revealed that the assembly is 100% complete, considering 460 marker genes from Streptomycetaceae family.

Table 1
Summary of genome features of Streptomyces sp F1.

Streptomyces sp. F1 showed highest 16S rDNA sequence similarity with Streptomyces misionensis strain NRRL B-3230T. In silico DNA-DNA hybridization (DDH)1212 Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics. 2013;14:60. and Average Nucleotide Identity/Alignment fraction (gANI/AF)1313 Varghese NJ, Mukherjee S, Ivanova N, et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res. 2015;43(14):6761-6771. values of Streptomyces sp. F1 compared to Streptomyces misionensis DSM 40306, were 94.2% and 99.4%/0.99, respectively, suggesting that strain F1 may be classified as Streptomyces misionensis.

Streptomyces sp. F1 genome was annotated using IMG-JGI Microbial Genome Annotation Pipeline (img.jgi.doe.gov). It has been predicted to include 7355 genes, being 7262 protein-coding genes, 3 rRNA (5S (1), 16S (1), 23S (1)), and 90 tRNA genes (Table 1). According to IMG functional annotation, 4453 genes were classified into COG categories, 5526 in PFAM protein families, 1542 in TIGRFAM families, and 714 in Transporter Classification. Further classification according to dbCAN showed that 175 proteins were classified as Carbohydrate-Active Enzymes, being 85 glycoside hydrolases organized in 33 distinct families. The current genome assembly provides a preliminary landscape of the genomic and metabolic capabilities of Streptomyces sp. F1.

Nucleotide sequence accession number

The whole genome sequences of Streptomyces sp. F1 have been deposited at DDBJ/EMBL/GenBank under accession number FKJI03000000.

Acknowledgements

The authors gratefully acknowledge the Brazilian National Council for Scientific and Technological Development (CNPq) for their financial support and fellowships, and CNPEM-CTBE for the use of Sequencing and Robotics NGS facility.

References

  • 1
    Barbe V, Bouzon M, Mangenot S, et al. Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. J Bacteriol 2011;193(18):5055-5056.
  • 2
    Takasuka TE, Book AJ, Lewin GR, Currie CR, Fox BG. Aerobic deconstruction of cellulosic biomass by an insect-associated Streptomyces Sci Rep. 2013;3:1030.
  • 3
    Chater KF, Biró S, Lee KJ, Palmer T, Schrempf H. The complex extracellular biology of Streptomyces FEMS Microbiol Rev 2010;34(2):171-198.
  • 4
    Franco-Cirigliano MN, Rezende RDC, Gravina-Oliveira MP, et al. Streptomyces misionensis PESB-25 produces a thermoacidophilic endoglucanase using sugarcane bagasse and corn steep liquor as the sole organic substrates. Biomed Res Int 2013;2013:1-10.
  • 5
    Wibberg D, Al-Dilaimi A, Busche T, et al. Complete genome sequence of Streptomyces reticuli, an efficient degrader of crystalline cellulose. J Biotechnol Elsevier BV 2016;222:13-14.
  • 6
    Book AJ, Lewin GR, McDonald BR, et al. Cellulolytic Streptomyces strains associated with herbivorous insects share a phylogenetically linked capacity to degrade lignocellulose. Appl Environ Microbiol 2014;80(15):4692-4701.
  • 7
    Semêdo LTAS, Gomes RC, Linhares AA, et al. Streptomyces drozdowiczii sp. nov., a novel cellulolytic streptomycete from soil in Brazil. Int J Syst Evol Microbiol 2004;54(4):1323-1328.
  • 8
    Horn S, Vaaje-Kolstad G, Westereng B, Eijsink VG. Novel enzymes for the degradation of cellulose. Biotechnol Biofuels 2012;5(1):45.
  • 9
    Bolger AM, Lohse M, Trimmomatic Usadel B. A flexible trimmer for Illumina Sequence Data. Bioinforma Adv 2014;30:2114.
  • 10
    Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19(5):455-477.
  • 11
    Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW, Check M. Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015;25(7):1043-1055.
  • 12
    Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14:60.
  • 13
    Varghese NJ, Mukherjee S, Ivanova N, et al. Microbial species delineation using whole genome sequences. Nucleic Acids Res 2015;43(14):6761-6771.

Publication Dates

  • Publication in this collection
    Oct-Dec 2017

History

  • Received
    26 Sept 2016
  • Accepted
    22 Nov 2016
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