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The Draft Genome Sequence and Analysis of an Efficiently Chitinolytic Bacterium Chitinibacter sp. Strain GC72

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Abstract

A novel chitinolytic bacterium Chitinibacter sp. GC72, which produces an enzyme capable of efficiently converting chitin only into N-acetyl-D-glucosamine (GlcNAc), was successfully sequenced and analyzed. The assembled draft genome of strain GC72 is 3,455,373 bp, containing 3346 encoded protein sequences with G + C content of 53.90%. Among these annotated genes, 17 chitinolytic enzymes including 12 glycoside hydrolase family 18 chitinases, three family 19 chitinases, one family 20 β-hexosaminidase, and one auxiliary activity family 10 lytic polysaccharide monooxygenase, were found to be essential in the production of GlcNAc from chitin. The genomic information of strain GC72 provides a reference genome for Chitinibacter bacteria and abundant novel chitinolytic enzyme resources, and allows researchers to explore potential applications in GlcNAc enzymatic production.

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References

  1. Rinaudo M (2006) Chitin and chitosan: properties and applications. Prog Polym Sci 31(7):603–632. https://doi.org/10.1016/j.progpolymsci.2006.06.001

    Article  CAS  Google Scholar 

  2. Yan N, Chen X (2015) Don't waste seafood waste. Nature 524(7564):155–157. https://doi.org/10.1038/524155a

    Article  CAS  PubMed  Google Scholar 

  3. Chen J-K, Shen C-R, Liu C-L (2010) N-Acetylglucosamine: production and applications. Mar Drugs 8(9):2493–2516. https://doi.org/10.3390/md8092493

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  4. Liu L, Liu Y, Shin H-d, Chen R, Li J, Du G, Chen J (2013) Microbial production of glucosamine and N-acetylglucosamine: advances and perspectives. Appl Microbiol and Biot 97(14):6149–6158. https://doi.org/10.1007/s00253-013-4995-6

    Article  CAS  Google Scholar 

  5. Kim TI, Ki KS, Dong HL, Vijayakumar M, Park SM, Sun HC, Kim KY, Im SK, Park BY (2017) Novel Acinetobacter parvus HANDI 309 microbial biomass for the production of N -acetyl-β- d -glucosamine (GlcNAc) using swollen chitin substrate in submerged fermentation. Biotechnol Biofuels 10(1):59. https://doi.org/10.1186/s13068-017-0740-1

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Dahiya N, Tewari R, Hoondal GS (2006) Biotechnological aspects of chitinolytic enzymes: a review. Appl Microbiol Biot 71(6):773–782. https://doi.org/10.1007/s00253-005-0183-7

    Article  CAS  Google Scholar 

  7. Sashiwa H, Fujishima S, Yamano N, Kawasaki N, Nakayama A, Muraki E, Hiraga K, Oda K, Aiba S (2002) Production of N-acetyl-D-glucosamine from alpha-chitin by crude enzymes from Aeromonas hydrophila H-2330. Carbohyd Res 337(8):761–763. https://doi.org/10.1016/s0008-6215(02)00034-4

    Article  CAS  Google Scholar 

  8. Moon C, Seo DJ, Song YS, Hong SH, Choi SH, Jung WJ (2017) Antifungal activity and patterns of N-acetyl-chitooligosaccharide degradation via chitinase produced from Serratia marcescens PRNK-1. Microb Pathog 113:218–224. https://doi.org/10.1016/j.micpath.2017.10.039

    Article  CAS  PubMed  Google Scholar 

  9. Ueda J, Kurosawa N (2015) Characterization of an extracellular thermophilic chitinase from Paenibacillus thermoaerophilus strain TC22-2b isolated from compost. World J Microbiol Biotechnol 31(1):135–143. https://doi.org/10.1007/s11274-014-1754-5

    Article  CAS  PubMed  Google Scholar 

  10. Hao ZK, Cai YJ, Liao XR, Liang XH, Liu JY, Fang ZY, Hu MM, Zhang DB (2011) Chitinolyticbacter meiyuanensis SYBC-H1(T), Gen. Nov., sp Nov., a chitin-degrading bacterium isolated from soil. Curr Microbiol 62(6):1732–1738. https://doi.org/10.1007/s00284-011-9921-5

    Article  CAS  PubMed  Google Scholar 

  11. Gao C, Zhang A, Chen K, Hao Z, Tong J, Ouyang P (2015) Characterization of extracellular chitinase from Chitinibacter sp GC72 and its application in GlcNAc production from crayfish shell enzymatic degradation. Biochem Eng J 97:59–64. https://doi.org/10.1016/j.bej.2015.02.010

    Article  CAS  Google Scholar 

  12. Kim SK, Kim YH, Jeong YS, Na HB, Kim J, Baik KS, Yun HD, Lee J-K, Kim H (2012) Chitinibacter suncheonensis sp nov., a chitinolytic bacterium from a mud flat in Suncheon Bay. J Microbiol 50(6):1058–1062. https://doi.org/10.1007/s12275-012-2333-9

    Article  CAS  PubMed  Google Scholar 

  13. Chern LL, Stackebrandt E, Lee SF, Lee FL, Chen JK, Fu HM (2004) Chitinibacter tainanensis gen. nov., sp nov., a chitin-degrading aerobe from soil in Taiwan. Int J Syst Evol Microbiol 54:1387–1391. https://doi.org/10.1099/ijs.0.02834-0

    Article  CAS  PubMed  Google Scholar 

  14. Sheu SY, Li YS, Young CC, Chen WM (2016) Chitinibacter fontanus sp nov., isolated from a spring. Int J Syst Evol Microbiol 66:4262–4268. https://doi.org/10.1099/ijsem.0.001345

    Article  CAS  PubMed  Google Scholar 

  15. Schubert M, Lindgreen S, Orlando L (2016) AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Res Notes 9:88–88. https://doi.org/10.1186/s13104-016-1900-2

    Article  PubMed  PubMed Central  Google Scholar 

  16. Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, He G, Chen Y, Pan Q, Liu Y, Tang J, Wu G, Zhang H, Shi Y, Liu Y, Yu C, Wang B, Lu Y, Han C, Cheung DW, Yiu S-M, Peng S, Zhu X, Liu G, Liao X, Li Y, Yang H, Wang J, Lam T-W, Wang J (2012) SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. https://doi.org/10.1186/2047-217x-1-18

    Article  PubMed  PubMed Central  Google Scholar 

  17. Coil D, Jospin G, Darling AE (2015) A5-miseq: an updated pipeline to assemble microbial genomes from Illumina MiSeq data. Bioinformatics 31(4):587–589. https://doi.org/10.1093/bioinformatics/btu661

    Article  CAS  PubMed  Google Scholar 

  18. Jones P, Binns D, Chang H-Y, Fraser M, Li W, McAnulla C, McWilliam H, Maslen J, Mitchell A, Nuka G, Pesseat S, Quinn AF, Sangrador-Vegas A, Scheremetjew M, Yong S-Y, Lopez R, Hunter S (2014) InterProScan 5: genome-scale protein function classification. Bioinformatics 30(9):1236–1240. https://doi.org/10.1093/bioinformatics/btu031

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017) A large-scale evaluation of algorithms to calculate average nucleotide identity. Anton Leeuw 110(10):1281–1286. https://doi.org/10.1007/s10482-017-0844-4

    Article  CAS  Google Scholar 

  20. Meier-Kolthoff JP, Auch AF, Klenk H-P, Goeker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. Bmc Bioinformatics. https://doi.org/10.1186/1471-2105-14-60

    Article  PubMed  PubMed Central  Google Scholar 

  21. Zhang AL, He YM, Wei GG, Zhou J, Dong WL, Chen KQ, Ouyang PK (2018) Molecular characterization of a novel chitinase CmChi1 from Chitinolyticbacter meiyuanensis SYBC-H1 and its use in N-acetyl-D-glucosamine production. Biotechnol Biofuels 11:14. https://doi.org/10.1186/s13068-018-1169-x

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Beier S, Bertilsson S (2013) Bacterial chitin degradation-mechanisms and ecophysiological strategies. Front Microbiol. https://doi.org/10.3389/fmicb.2013.00149

    Article  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported by the National Key Research and Development Program (2016YFA0204300), the National Natural Science Foundation of China (31700092), the National Nature Science Foundation for Young Scientists of China (Grant No. 21908101, 21576134), and China Postdoctoral Science Foundation (2018M642237, 2020T130295).

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Authors and Affiliations

  1. College of Biotechnology and Pharmaceutical Engineering, State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, Nanjing, 211800, People’s Republic of China

    Alei Zhang, Xiaofang Mo, Guoguang Wei, Ning Zhou, Sai Yang, Jie Chen, Yingying Wang, Kequan Chen & Pingkai Ouyang

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  1. Alei Zhang
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  2. Xiaofang Mo
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Correspondence to Kequan Chen.

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Zhang, A., Mo, X., Wei, G. et al. The Draft Genome Sequence and Analysis of an Efficiently Chitinolytic Bacterium Chitinibacter sp. Strain GC72. Curr Microbiol 77, 3903–3908 (2020). https://doi.org/10.1007/s00284-020-02215-9

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  • DOI: https://doi.org/10.1007/s00284-020-02215-9

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