Journal of Biotechnology 200 (2015) 77–78
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of Bacillus sp. YP1, a polyethylene-degrading bacterium from waxworm’s gut Yu Yang a , Jianwei Chen b , Wei-Min Wu c , Jiao Zhao b,∗∗ , Jun Yang a,∗ a Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry and Environment, Beihang University, Beijing 100191, PR China b Shenzhen Key Laboratory of Bioenergy, BGI, Shenzhen 518083, PR China c Department of Civil and Environmental Engineering, William & Cloy Codiga Resource Recovery Research Center, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, CA 94305-4020, USA
a r t i c l e
i n f o
Article history: Received 13 February 2015 Accepted 25 February 2015 Available online 18 March 2015 Keywords: Genome sequence Bacillus Biodegradation Polyethylene
a b s t r a c t Bacillus sp. strain YP1, isolated from the gut of waxworm (the larvae of Plodia interpunctella) which ate polyethylene (PE) plastic, is capable of degrading PE and utilizing PE as sole carbon source. Here we report the complete genome sequence of strain YP1, which is relevant to polyethylene depolymerization and biodegradation. © 2015 Published by Elsevier B.V.
Polyethylene (PE), expressed as “[CH2 CH2 ]n ”, is a widely used petroleum-based plastic. However, the obvious contrast between its resistance and the short service time of PE products leads to the accumulation of PE waste in the environment, which has generated global concern (Yang et al., 2014). Several properties of PE make it resistant to biodegradation. Among these properties are (a) PE’s high stable C C and C O covalent bonds; (b) its high molecular weight, which makes it too large to penetrate the cell wall of microbes; and (c) its highly hydrophobic nature. Many attempts found that the microbial cultures from natural environments have extremely limited ability to degrade PE because that these microorganisms lack the enzymes capable of oxidizing and depolymerizing the long carbon chain of PE (Restrepo-Flo´ırez et al., 2014). Bacillus sp. YP1, a Gram-positive and rod-shaped bacterium, is isolated from the guts of waxworms (the larvae of Plodia interpunctella) which are able to chew and eat PE films. Recently, we have demonstrated that Bacillus sp. YP1 is able to degrade
∗ Corresponding author at: School of Chemistry and Environment, Beihang University, 37 Xueyuan Road, Beijing 100191, PR China. Tel.: +86 1082338552. ∗∗ Corresponding author at: Shenzhen Key Laboratory of Bioenergy, 11 Beishan Industrial Park, Shenzhen 518083, PR China. E-mail addresses: [email protected] (J. Zhao), [email protected] (J. Yang). http://dx.doi.org/10.1016/j.jbiotec.2015.02.034 0168-1656/© 2015 Published by Elsevier B.V.
PE and use it as sole carbon source (Yang et al., 2014). Bacillus sp. strain YP1 can form viable biofilm on the PE film sheet covered mineral salt agar medium. The growth of biofilm of strain YP1 causes obvious damages of the PE film with appearance of newly carbonyl groups on the PE film surface. The strain YP1 depolymerizes long-chain macromolecular of PE into watersoluble low molecular weight products. Here, we report the complete genome sequence of Bacillus sp. strain YP1. The information of these genes helps to understand the genetic basis of PE-degrading activities and to discover the enzymes relevant to PE biodegradation. The genomic DNA of the strain YP1 was extracted by using a conventional proteinase K treatment and phenol–chloroform extraction. Genomic libraries containing 0.5, 2 and 6 kb inserts were constructed, and 1000 M high-quality base pairs, were generated at about 250-fold coverage of the genome by using Illumina Hiseq 2000 at BGI-Shenzhen, China. The pair-end reads were de novo assembled into 13 contigs (935,629, N50 Contig length) in 5 scaffolds using SOAPdenovo v.1.05 (Li et al., 2010). The complete genome was achieved by filling the gaps between the junctions of contigs, using general PCR and Sanger sequencing method. Gene prediction was determined by using Glimmer 3.0 (Delcher et al., 2007). Genes coding tRNA and rRNA genes were determined through tRNAscan-SE and RNAmmer, respectively (Lowe and Eddy, 1997; Lagesen et al., 2007). The G + C (mole percent) contents were calculated according to the genome sequences.
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Y. Yang et al. / Journal of Biotechnology 200 (2015) 77–78
Table 1 Bacillus sp. YP1 genome features. Characteristics
Total value
Chromosome
Plasmid
Size of genome (bp) G + C content (%) Coding density (%) No. of genes No. of function assigned protein No. of hypothetical protein With no database match No. of RNA genes No. of rRNA No. of tRNA
4,153,566 43.64 88.28 4238 2947 1129 41 121 30 87
4,070,380 43.81 88.47 4161 2905 1098 38 120 30 85
83,186 35.09 78.95 77 42 31 3 1 0 2
The complete strain YP1 genome contains a circular chromosome of 4,070,380 bp with a 43.81% G + C content, and a circular plasmid, pBUYP1of 83,186 bp with a 35.09% G + C content. A total of 4238 genes were predicted in strain YP1 genome. The genes were blasted against the COG databases. Total of 3038 genes were classified into 21 Clusters of Orthologous Groups (COG) categories. There were 87 tRNA genes and 30 rRNA loci were found, respectively (Table 1). The metabolic networks were found according to KEGG analysis. A total of 182 genes are involved in the pathway of biodegradation and metabolisms of xenobiotics. 1. Nucleotide sequence accession numbers These whole genome sequencing projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers CP010014–CP010015. Acknowledgments This work was supported by the National Natural Science Foundation of China (51373006 and 20477002), the State Basic Research
Program of China (2014CB931800) and Shenzhen Key Laboratory of Bioenergy (grant CXB201005240001A). This strain has been deposited at the China General Microbiological Culture Collection Center (CGMCC No.6319). References Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, R.Q., Zhu, H.M., Ruan, J., Qian, W.B., Fang, X.D., Shi, Z.B., Li, Y.R., Li, S.T., Shan, G., Kristiansen, K., Li, S.G., Yang, H.M., Wang, J., Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Restrepo-Flo´ırez, J.M., Bassi, A., Thompson, M.R., 2014. Microbial degradation and deterioration of polyethylene – a review. Int. Biodeterior. Biodegradation 88, 83–90. Yang, J., Yang, Y., Wu, W.M., Zhao, J., Jiang, L., 2014. Evidence of polyethylene biodegradation by bacterial strains from the guts of plastic-eating waxworms. Environ. Sci. Technol. 48 (23), 13776–13784.
Contents lists available at ScienceDirect
Journal of Biotechnology journal homepage: www.elsevier.com/locate/jbiotec
Genome Announcement
Complete genome sequence of Bacillus sp. YP1, a polyethylene-degrading bacterium from waxworm’s gut Yu Yang a , Jianwei Chen b , Wei-Min Wu c , Jiao Zhao b,∗∗ , Jun Yang a,∗ a Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology of Ministry of Education, School of Chemistry and Environment, Beihang University, Beijing 100191, PR China b Shenzhen Key Laboratory of Bioenergy, BGI, Shenzhen 518083, PR China c Department of Civil and Environmental Engineering, William & Cloy Codiga Resource Recovery Research Center, Center for Sustainable Development & Global Competitiveness, Stanford University, Stanford, CA 94305-4020, USA
a r t i c l e
i n f o
Article history: Received 13 February 2015 Accepted 25 February 2015 Available online 18 March 2015 Keywords: Genome sequence Bacillus Biodegradation Polyethylene
a b s t r a c t Bacillus sp. strain YP1, isolated from the gut of waxworm (the larvae of Plodia interpunctella) which ate polyethylene (PE) plastic, is capable of degrading PE and utilizing PE as sole carbon source. Here we report the complete genome sequence of strain YP1, which is relevant to polyethylene depolymerization and biodegradation. © 2015 Published by Elsevier B.V.
Polyethylene (PE), expressed as “[CH2 CH2 ]n ”, is a widely used petroleum-based plastic. However, the obvious contrast between its resistance and the short service time of PE products leads to the accumulation of PE waste in the environment, which has generated global concern (Yang et al., 2014). Several properties of PE make it resistant to biodegradation. Among these properties are (a) PE’s high stable C C and C O covalent bonds; (b) its high molecular weight, which makes it too large to penetrate the cell wall of microbes; and (c) its highly hydrophobic nature. Many attempts found that the microbial cultures from natural environments have extremely limited ability to degrade PE because that these microorganisms lack the enzymes capable of oxidizing and depolymerizing the long carbon chain of PE (Restrepo-Flo´ırez et al., 2014). Bacillus sp. YP1, a Gram-positive and rod-shaped bacterium, is isolated from the guts of waxworms (the larvae of Plodia interpunctella) which are able to chew and eat PE films. Recently, we have demonstrated that Bacillus sp. YP1 is able to degrade
∗ Corresponding author at: School of Chemistry and Environment, Beihang University, 37 Xueyuan Road, Beijing 100191, PR China. Tel.: +86 1082338552. ∗∗ Corresponding author at: Shenzhen Key Laboratory of Bioenergy, 11 Beishan Industrial Park, Shenzhen 518083, PR China. E-mail addresses: [email protected] (J. Zhao), [email protected] (J. Yang). http://dx.doi.org/10.1016/j.jbiotec.2015.02.034 0168-1656/© 2015 Published by Elsevier B.V.
PE and use it as sole carbon source (Yang et al., 2014). Bacillus sp. strain YP1 can form viable biofilm on the PE film sheet covered mineral salt agar medium. The growth of biofilm of strain YP1 causes obvious damages of the PE film with appearance of newly carbonyl groups on the PE film surface. The strain YP1 depolymerizes long-chain macromolecular of PE into watersoluble low molecular weight products. Here, we report the complete genome sequence of Bacillus sp. strain YP1. The information of these genes helps to understand the genetic basis of PE-degrading activities and to discover the enzymes relevant to PE biodegradation. The genomic DNA of the strain YP1 was extracted by using a conventional proteinase K treatment and phenol–chloroform extraction. Genomic libraries containing 0.5, 2 and 6 kb inserts were constructed, and 1000 M high-quality base pairs, were generated at about 250-fold coverage of the genome by using Illumina Hiseq 2000 at BGI-Shenzhen, China. The pair-end reads were de novo assembled into 13 contigs (935,629, N50 Contig length) in 5 scaffolds using SOAPdenovo v.1.05 (Li et al., 2010). The complete genome was achieved by filling the gaps between the junctions of contigs, using general PCR and Sanger sequencing method. Gene prediction was determined by using Glimmer 3.0 (Delcher et al., 2007). Genes coding tRNA and rRNA genes were determined through tRNAscan-SE and RNAmmer, respectively (Lowe and Eddy, 1997; Lagesen et al., 2007). The G + C (mole percent) contents were calculated according to the genome sequences.
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Y. Yang et al. / Journal of Biotechnology 200 (2015) 77–78
Table 1 Bacillus sp. YP1 genome features. Characteristics
Total value
Chromosome
Plasmid
Size of genome (bp) G + C content (%) Coding density (%) No. of genes No. of function assigned protein No. of hypothetical protein With no database match No. of RNA genes No. of rRNA No. of tRNA
4,153,566 43.64 88.28 4238 2947 1129 41 121 30 87
4,070,380 43.81 88.47 4161 2905 1098 38 120 30 85
83,186 35.09 78.95 77 42 31 3 1 0 2
The complete strain YP1 genome contains a circular chromosome of 4,070,380 bp with a 43.81% G + C content, and a circular plasmid, pBUYP1of 83,186 bp with a 35.09% G + C content. A total of 4238 genes were predicted in strain YP1 genome. The genes were blasted against the COG databases. Total of 3038 genes were classified into 21 Clusters of Orthologous Groups (COG) categories. There were 87 tRNA genes and 30 rRNA loci were found, respectively (Table 1). The metabolic networks were found according to KEGG analysis. A total of 182 genes are involved in the pathway of biodegradation and metabolisms of xenobiotics. 1. Nucleotide sequence accession numbers These whole genome sequencing projects have been deposited at DDBJ/EMBL/GenBank under the accession numbers CP010014–CP010015. Acknowledgments This work was supported by the National Natural Science Foundation of China (51373006 and 20477002), the State Basic Research
Program of China (2014CB931800) and Shenzhen Key Laboratory of Bioenergy (grant CXB201005240001A). This strain has been deposited at the China General Microbiological Culture Collection Center (CGMCC No.6319). References Delcher, A.L., Bratke, K.A., Powers, E.C., Salzberg, S.L., 2007. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23, 673–679. Lagesen, K., Hallin, P., Rødland, E.A., Staerfeldt, H.H., Rognes, T., Ussery, D.W., 2007. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 35, 3100–3108. Li, R.Q., Zhu, H.M., Ruan, J., Qian, W.B., Fang, X.D., Shi, Z.B., Li, Y.R., Li, S.T., Shan, G., Kristiansen, K., Li, S.G., Yang, H.M., Wang, J., Wang, J., 2010. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 20, 265–272. Lowe, T.M., Eddy, S.R., 1997. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 25, 955–964. Restrepo-Flo´ırez, J.M., Bassi, A., Thompson, M.R., 2014. Microbial degradation and deterioration of polyethylene – a review. Int. Biodeterior. Biodegradation 88, 83–90. Yang, J., Yang, Y., Wu, W.M., Zhao, J., Jiang, L., 2014. Evidence of polyethylene biodegradation by bacterial strains from the guts of plastic-eating waxworms. Environ. Sci. Technol. 48 (23), 13776–13784.
