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Genome sequencing of strain Cellulosimicrobium sp. TH-20 with ginseng biotransformation ability

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Abstract

Biotransformation for increasing the pharmaceutical effect of ginsenosides is getting more and more attractions. Strain Cellulosimicrobium sp. TH-20 isolated from ginseng soil samples was identified to produce enzymes contributing to its excellent biotransformation activity against ginsenosides, the main active components of ginseng. Based on phylogenetic tree and homology analysis, the strain can be designated as Cellulosimicrobium sp. Genome sequencing was performed using the Illumina Miseq to explore the functional genes involved in ginsenoside transformation. The draft genome of Cellulosimicrobium sp. TH-20 encoded 3450 open reading frames, 51 tRNA, and 9 rRNA. All ORFs were annotated using NCBI BLAST with non-redundant proteins, Gene Ontology, Cluster of Orthologous Gene, and Kyoto Encyclopedia of Genes and Genomes databases. A total of 11 genes were selected based on the functional annotation analysis. These genes are relevant to ginsenoside biotransformation, including 6 for beta-glucosidase, 1 for alpha-N-arabinofuranosidase, 1 for alpha-1,6-glucosidase, 1 for endo-1,4-beta-xylanase, 1 for alpha-l-arabinofuranosidase, and 1 for beta-galactosidase. These glycosidases were predicted to catalyze the hydrolysis of sugar moieties attached to the aglycon of ginsenosides and led to the transformation of PPD-type and PPT-type ginsenosides.

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References

  • An DS, Cui CH, Lee HG, Wang L, Kim SC, Lee ST, Jin F, Yu H, Chin YW, Lee HK, Im WT, Kim SG (2010) Identification and characterization of a novel Terrabacter ginsenosidimutans sp. nov. β-glucosidase that transforms ginsenoside Rb1 into the rare gypenosides XVII and LXXV. Appl Environ Microbiol 76:5827–5836

    Article  CAS  Google Scholar 

  • Chen G, Yang M, Lu Z, Zhang J, Huang H, Liang Y, Guan S, Song Y, Wu L, Guo DA (2007) Microbial transformation of 20(S)-protopanaxatriol-type saponins by Absidia coerulea. J Nat Prod 70:1203–1206

    Article  CAS  Google Scholar 

  • Chen GT, Yang M, Song Y, Lu ZQ, Zhang JQ, Huang HL, Wu LJ, Guo DA (2008) Microbial transformation of ginsenoside Rb(1) by Acremonium strictum. Appl Microbiol Biotechnol 77:1345–1350

    Article  CAS  Google Scholar 

  • Cheng LQ, Kim MK, Lee JW, Lee YJ, Yang DC (2006) Conversion of major ginsenoside Rb1 to ginsenoside F2 by Caulobacter leidyia. Biotechnol Lett 28:1121–1127

    Article  CAS  Google Scholar 

  • Cheng LQ, Na JR, Kim MK, Bang MH, Yang DC (2007) Microbial conversion of ginsenoside Rb1 to minor ginsenoside F2 and gypenoside XVII by Intrasporangium sp. GS603 isolated from soil. J Microbiol Biotechnol 17:1937–1943

    CAS  Google Scholar 

  • Cheng LQ, Na JR, Bang MH, Kim MK, Yang DC (2008) Conversion of major ginsenoside Rb1 to 20(S)-ginsenoside Rg3 by Microbacterium sp. GS514. Phytochemistry 69:218–224

    Article  CAS  Google Scholar 

  • Cui CH, Kim SC, Im WT (2013) Characterization of the ginsenoside-transforming recombinant β-glucosidase from Actinosynnema mirum and bioconversion of major ginsenosides into minor ginsenosides. Appl Microbiol Biotechnol 97:649–659

    Article  CAS  Google Scholar 

  • Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with glimmer. Bioinformatics 23:673–679

    Article  CAS  Google Scholar 

  • Dong A, Ye M, Guo H, Zheng J, Guo D (2003) Microbial transformation of ginsenoside Rb1 by Rhizopus stolonifer and Curvularia lunata. Biotechnol Lett 25:339–344

    Article  CAS  Google Scholar 

  • Feng L, Xu C, Li Z, Li J, Dai Y, Han H, Yu S, Liu S (2015) Microbial conversion of ginsenoside Rd from Rb1 by the fungus mutant Aspergillus niger strain TH-10a. Prep Biochem Biotechnol 46:336–441

    Article  Google Scholar 

  • Fu Y, Cheng L, Meng Y, Li S, Zhao X, Du Y, Yin H (2015) Cellulosimicrobium cellulans strain E4-5 enzymatic hydrolysis of curdlan for production of (1 → 3)-linked β-d-glucan oligosaccharides. Carbohyd Polym 134:740–744

    Article  CAS  Google Scholar 

  • Hou JG, Xue JJ, Sun MQ, Wang CY, Liu L, Zhang DL, Lee MR, Gu LJ, Wang CL, Wang YB, Zheng Y, Li W, Sung CK (2012) Highly selective microbial transformation of major ginsenoside Rb1 to gypenoside LXXV by Esteya vermicola CNU120806. J Appl Microbiol 113:807–821

    Article  CAS  Google Scholar 

  • Hou JG, Xue JJ, Sun MQ, Wang CY, Liu L, Zhang DL, Lee MR, Gu LJ, Wang CL, Wang YB, Zheng Y, Li W, Sung CK (2015) Highly selective microbial transformation of major ginsenoside Rb1 to gypenoside LXXV by Esteya vermicola CNU120806. J Appl Microbiol 113:807–821

    Article  Google Scholar 

  • Hyun YJ, Kim B, Kim DH (2012) Cloning and characterization of ginsenoside Ra1-hydrolyzing beta-d-xylosidase from Bifidobacterium breve K-110. J Microbiol Biotechnol 22:535–575

    Article  CAS  Google Scholar 

  • Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M (2004) The KEGG resource for deciphering the genome. Nucleic Acids Res 32:D277–D280

    Article  CAS  Google Scholar 

  • Karthik C, Oves M, Thangabalu R, Sharma R, Santhosh SB, Indra Arulselvi P (2016) Cellulosimicrobium funkei-like enhances the grow of Phaseolus vulgaris by modulating oxidative damage under chromium (VI) toxicity. J Adv Res 7:839–850

    Article  CAS  Google Scholar 

  • Kim MK, Lee JW, Lee KY, Yang DC (2005) Microbial conversion of major ginsenoside Rb1 to pharmaceutically active minor ginsenoside Rd. J Microbiol 43:456–462

    CAS  Google Scholar 

  • Koren S, Schatz MC, Walenz BP, Martin J, Howard JT, Ganapathy G, Wang Z, Rasko DA, McCombie WR, Jarvis ED, Phillippy Adam M (2012) Hybrid error correction and de novo assembly of single-molecule sequencing reads. Nat Biotechnol 30:693–700

    Article  CAS  Google Scholar 

  • Liang WG, Liu QM, Sung BH (2011) Bioconversion of ginsenosides Rb1, Rb2, Rc and Rd by novel-glucosidase hydrolyzing outer 3-O glycoside from Sphingomonas sp. 2F2: cloning, expression, and enzyme characterization. J Biotechnol 156:125–133

    Article  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  Google Scholar 

  • Noh KH, Oh DK (2009) Production of the rare ginsenosides compound K, compound Y, and compound Mc by a thermostable β-glycosidase from Sulfolobus acidocaldarius. Biol Pharm Bull 32:1830–1835

    Article  CAS  Google Scholar 

  • Noh KH, Son JW, Kim HJ, Oh DK (2009) Ginsenoside compound K production from ginseng root extract by a thermostable β-glycosidase from Sulfolobus solfataricus. Biosci Biotechnol Biochem 73:316–321

    Article  CAS  Google Scholar 

  • Oh HJ, Shin KC, Oh DK (2014) Production of ginsenosides Rg1 and Rh1 by hydrolyzing the outer glycoside at the C-6 position in protopanaxatriol-type ginsenosides using β-glucosidase from Pyrococcus furiosus. Biotech Lett 36:113–119

    Article  CAS  Google Scholar 

  • Quan LH, Jin Y, Wang C, Min JW, Kim YJ, Yang DC (2012) Enzymatic transformation of the major ginsenoside Rb2 to minor compound Y and compound K by a ginsenoside-hydrolyzing β-glycosidase from Microbacterium esteraromaticum. J Ind Microbiol Biotechnol 39:1557–1562

    Article  CAS  Google Scholar 

  • Ru W, Wang D, Xu Y, He X, Sun YE, Qian L, Zhou X, Qin Y (2015) Chemical constituents and bioactivities of Panax ginseng (C.A. Mey.). Drug Discov Ther 9:23–32

    Article  Google Scholar 

  • Ruan CC, Zhang H, Zhang LX, Liu Z, Sun GZ, Lei J, Qin YX, Zheng YN, Li X, Pan HY (2009) Biotransformation of ginsenoside Rf to Rh1 by recombinant β-glucosidase. Molecules 14:2043–2048

    Article  CAS  Google Scholar 

  • Schumann P, Weiss N, Stackebrandt E (2001) Reclassification of Cellulomonas cellulans (Stackebrandt and Keddie 1986) as Cellulosimicrobium cellulans gen. nov., comb. nov. Int J Syst Evol Microbiol 51:1007–1017

    Article  CAS  Google Scholar 

  • Sharma A, Hira P, Shakarad M, Lal R (2014) Draft genome sequence of Cellulosimicrobium sp. strain MM, isolated from arsenic-rich microbial mats of a Himalayan hot spring. Genome Announc 2:e01020–e01034

    Google Scholar 

  • Sharma A, Gilbert JA, Lal R (2016) (Meta) genomic insights into the pathogenome of Cellulosimicrobium cellulans. Sci Rep 6:25527

    Article  CAS  Google Scholar 

  • Shin KC, Seo MJ, Oh HJ, Oh DK (2009) A novel ginsenoside Rb1-hydrolyzing β-d-glucosidase from Cladosporium fulvum. Process Biochem 36:1287–1293

    Google Scholar 

  • Shin KC, Oh HJ, Kim BJ, Oh DK (2013) Complete conversion of major protopanaxadiol ginsenosides to compound K by the combined use of α-l-arabinofuranosidase and β-galactosidase from Caldicellulosiruptor saccharolyticus and β-glucosidase from Sulfolobus acidocaldarius. J Biotechnol 167:33–40

    Article  CAS  Google Scholar 

  • Shin KC, Seo MJ, Oh HJ, Oh DK (2014) Highly selective hydrolysis for the outer glucose at the C-20 position in ginsenosides by β-glucosidase from Thermus thermophilus and its application to the production of ginsenoside F2 from gypenoside XVII. Biotechnol Lett 36:1287–1293

    Article  CAS  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599

    Article  CAS  Google Scholar 

  • Tanabe Y, Oda M (2011) Molecular characterization of endo-1,3-β-glucanase from Cellulosimicrobium cellulans: effects of carbohydrate-binding module on enzymatic function and stability. Biochim Biophys Acta 1814:1713–1722

    Article  CAS  Google Scholar 

  • Wei Y, Zhao W, Zhang Q, Zhao Y, Zhang Y (2011) Purification and characterization of a novel and unique ginsenoside Rg1-hydrolyzing β-d-glucosidase from Penicillium sclerotiorum. Acta Biochim Biophys Sin 43:226–231

    Article  CAS  Google Scholar 

  • Yuan Y, Hu YB, Hu CX (2015) Overexpression and characterization of a glycoside hydrolase family 1 enzyme from Cellulosimicrobium cellulans sp.21 and its application for minor ginsenosides production. J Mol Catal B Enzym 120:60–67

    Article  CAS  Google Scholar 

  • Zhou W, Yan Q, Li JY, Zhang XC, Zhou P (2008) Biotransformation of Panax noto ginseng saponins into ginsenoside compound K production by Paecilomyces bainier sp. 229. J Appl Microbiol 104:699–706

    Article  CAS  Google Scholar 

  • Zhou M, Liu Q, Xie Y, Dong B, Chen X (2016) Draft genome sequence of Thermococcus sp. EP1, a novel hyperthermophilic archaeon isolated from a deep-sea hydrothermal vent on the East Pacific Rise. Marine Genom 26:9–11

    Article  Google Scholar 

Download references

Acknowledgements

This research was supported by the National Natural Science Foundation of China (No. 3140040275).

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Authors and Affiliations

  1. Jilin Ginseng Academy, Changchun University of Chinese Medicine, Changchun, 130117, China

    Fei Zheng, Yulin Dai, Jing Li, Huanxi Zhao, Hao Yue & Shanshan Yu

  2. The Affiliated Hospital of Changchun University of Chinese Medicine, Changchun, 130117, China

    Wei Zhang

  3. Life Science Research Center, Beihua University, Jilin, 132011, China

    Xiaodan Chu

  4. College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, China

    Fei Zheng & Liankui Wen

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  1. Fei Zheng
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  2. Wei Zhang
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  8. Hao Yue
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Correspondence to Hao Yue or Shanshan Yu.

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Zheng, F., Zhang, W., Chu, X. et al. Genome sequencing of strain Cellulosimicrobium sp. TH-20 with ginseng biotransformation ability. 3 Biotech 7, 237 (2017). https://doi.org/10.1007/s13205-017-0850-2

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