Abstract
Chitooligosaccharides have important application value in the fields of food and agriculture. Chitosanase can degrade chitosan to obtain chitooligosaccharides. The marine metagenome contains many genes related to the degradation of chitosan. However, it is difficult to mine valuable genes from large gene resources. This study proposes a method to screen chitosanases directly from the marine metagenome. Chitosanase gene chis1754 was identified from the metagenome and heterologously expressed in Escherichia coli. The optimal temperature and pH of CHIS1754 were 55 °C and 5.5, respectively. A mutant, CHIS1754T, with 15 single point mutations designed based on molecular evolution data was also expressed in E. coli. The results indicated that the thermal stability of CHIS1754T was significantly improved, as the Tm showed an increase of ~ 7.63 °C. Additionally, the kcat/Km of CHIS1754T was 4.8-fold higher than that of the wild type. This research provides new theories and foundations for the excavation, modification, and industrial application of chitosanases.
Key points
-
A chitosanase gene, chis1754, was firstly identified from marine metagenome.
-
A multi-site mutant was designed to improve enzyme stability and activity.
-
The kcat/Kmof the designed mutant was 4.8-fold higher than that of the wild type.
Similar content being viewed by others
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/s0022-2836(05)80360-2
Araújo NKD, Pagnoncelli MGB, Pimentel VC, Xavier MLO, Padilha CEA, Macedo GRD, Santos ESD (2016) Single-step purification of chitosanases from Bacillus cereus using expanded bed chromatography. Int J Biol Macromol 82:291–298. https://doi.org/10.1016/j.ijbiomac.2015.09.063
Azuma K, Osaki T, Kurozumi S, Kiyose M, Tsuka T, Murahata Y, Imagawa T, Itoh N, Minami S, Sato K (2015) Anti-inflammatory effects of orally administered glucosamine oligomer in an experimental model of inflammatory bowel disease. Carbohydr Polym 115:448–456. https://doi.org/10.1016/j.carbpol.2014.09.012
Chang Y, Chung Y, Hsu C, Chen L, Chiang C, Chang C, Sung H (2011) Biochemical characterization of a β-N-acetylhexosaminidase from fig latex. Bot Stu 52(1):23–34 http://ntur.lib.ntu.edu.tw/handle/246246/243145
Chang M, Chu X, Lv J, Li Q, Tian J, Wu N (2016) Improving the thermostability of acidic pullulanase from Bacillus naganoensis by rational design. PLoS One 11(10):e0165006. https://doi.org/10.1371/journal.pone.0165006
de Hoon MJ, Imoto S, Nolan J, Miyano S (2004) Open source clustering software. Bioinformatics 20(9):1453–1454. https://doi.org/10.1093/bioinformatics/bth078
Durowoju IB, Bhandal KS, Hu J, Carpick B, Kirkitadze M (2017) Differential scanning calorimetry - a method for assessing the thermal stability and conformation of protein antigen. J Vis Exp 121:e55262. https://doi.org/10.3791/55262
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32(5):1792–1797. https://doi.org/10.1093/nar/gkh340
Fernandes JC, Tavaria FK, Fonseca SC, Ramos OS, Pintado ME, Malcata FX (2010) In vitro screening for anti-microbial activity of chitosans and chitooligosaccharides, aiming at potential uses in functional textiles. J Microbiol Biotechnol 20(2):311–318. https://doi.org/10.4014/jmb.0904.04038
Finn RD, Clements J, Eddy SR (2011) HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39(Web Server issue):W29–W37. https://doi.org/10.1093/nar/gkr367
Francesko A, Tzanov T (2011) Chitin, chitosan and derivatives for wound healing and tissue engineering. Adv Biochem Eng Biotechnol 125:1–27. https://doi.org/10.1007/10_2010_93
Gribenko AV, Patel MM, Liu J, McCallum SA, Wang C, Makhatadze GI (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions. Proc Natl Acad Sci USA 106(8):2601–2606. https://doi.org/10.1073/pnas.0808220106
Han Y, Gao P, Yu W, Lu X (2017) Thermostability enhancement of chitosanase CsnA by fusion a family 5 carbohydrate-binding module. Biotechnol Lett 39(12):1895–1901. https://doi.org/10.1007/s10529-017-2406-2
Han Y, Gao P, Yu W, Lu X (2018) N-Terminal seven-amino-acid extension simultaneously improves the pH stability, optimal temperature, thermostability and catalytic efficiency of chitosanase CsnA. Biotechnol Lett 40(1):75–82. https://doi.org/10.1007/s10529-017-2436-9
Jin Q, Yu H, Wang X, Li K, Li P (2017) Effect of the molecular weight of water-soluble chitosan on its fat-/cholesterol-binding capacities and inhibitory activities to pancreatic lipase. PeerJ 5:e3279. https://doi.org/10.7717/peerj.3279
Jing W, Jiquan Z, Fengge S, Tianshu G, Jianhai X (2015) Purification and characterization of chitinases from ridgetail white prawn Exopalaemon carinicauda. Molecules (Basel, Switzerland) 20(2):1955–1967. https://doi.org/10.3390/molecules20021955
Jun W, Wei Z, Hang Y, Yujuan W (2008) Characterization of a novel fungal chitosanase Csn2 from Gongronella sp. JG. Carbohydr Res 343(15):2583–2588. https://doi.org/10.1016/j.carres.2008.08.004
Jung WJ, Park RD (2014) Bioproduction of chitooligosaccharides: present and perspectives. Mar Drugs 12(11):5328–5356. https://doi.org/10.3390/md12115328
Kaczmarek MB, Struszczyk-Swita K, Li X, Szczęsna-Antczak M, Daroch M (2019) Enzymatic modifications of chitin, chitosan, and chitooligosaccharides. Front Bioeng Biotechnol 7:243. https://doi.org/10.3389/fbioe.2019.00243
Karin M, Clevers H (2016) Reparative inflammation takes charge of tissue regeneration. Nature 529(7586):307–315. https://doi.org/10.1038/nature17039
Kumar S, Tsai CJ, Nussinov R (2000) Factors enhancing protein thermostability. Protein Eng 13(3):179–191. https://doi.org/10.1093/protein/13.3.179
Kumwenda B, Litthauer D, Bishop OT, Reva O (2013) Analysis of protein thermostability enhancing factors in industrially important Thermus bacteria species. Evol Bioinform Online 9:327–342. https://doi.org/10.4137/ebo.S12539
Lai P, Shiau CJ, Wang CC (2012) Effects of oligosaccharides on phase transition temperatures and rheological characteristics of waxy rice starch dispersion. J Sci Food Agric 92(7):1389–1394. https://doi.org/10.1002/jsfa.4712
Li K, Xing R, Liu S, Li P (2016) Advances in preparation, analysis and biological activities of single chitooligosaccharides. Carbohydr Polym 139(2016):178–190. https://doi.org/10.1016/j.carbpol.2015.12.016
Liang TW, Chen WT, Lin ZH, Kuo YH, Nguyen AD, Pan PS, Wang SL (2016) An amphiprotic novel chitosanase from Bacillus mycoides and its application in the production of chitooligomers with their antioxidant and anti-inflammatory evaluation. Int J Mol Sci 17(8). https://doi.org/10.3390/ijms17081302
Liang S, Sun Y, Dai X (2018) A review of the preparation, analysis and biological functions of chitooligosaccharide. Int J Mol Sci 19(8):2197. https://doi.org/10.3390/ijms19082197
Luo C, Liu W, Luo B, Tian J, Wen W, Liu M, Zhou C (2017) Antibacterial activity and cytocompatibility of chitooligosaccharide-modified polyurethane membrane via polydopamine adhesive layer. Carbohydr Polym 156:235–243. https://doi.org/10.1016/j.carbpol.2016.09.036
Marcotte EM, Monzingo AF, Ernst SR, Brzezinski R, Robertus JD (1996) X-ray structure of an anti-fungal chitosanase from Streptomyces N174. Nat Struct Biol 3(2):155–162. https://doi.org/10.1038/nsb0296-155
Muanprasat C, Chatsudthipong V (2016) Chitosan oligosaccharide: biological activities and potential therapeutic applications. Pharmacol Ther 170:80–97. https://doi.org/10.1016/j.pharmthera.2016.10.013
Needleman SB, Wunsch CD (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48(3):443–453. https://doi.org/10.1016/0022-2836(70)90057-4
Nguyen AD, Huang CC, Liang TW, Nguyen VB, Pan PS, Wang SL (2014) Production and purification of a fungal chitosanase and chitooligomers from Penicillium janthinellum D4 and discovery of the enzyme activators. Carbohydr Polym 108:331–337. https://doi.org/10.1016/j.carbpol.2014.02.053
Nguyen HM, Mathiesen G, Stelzer EM, Pham ML, Kuczkowska K, Mackenzie A, Agger JW, Eijsink VG, Yamabhai M, Peterbauer CK, Haltrich D, Nguyen TH (2016) Display of a beta-mannanase and a chitosanase on the cell surface of Lactobacillus plantarum towards the development of whole-cell biocatalysts. Microb Cell Fact 15(1):169. https://doi.org/10.1186/s12934-016-0570-z
Pell G, Taylor EJ, Gloster TM, Turkenburg JP, Fontes CM, Ferreira LM, Nagy T, Clark SJ, Davies GJ, Gilbert HJ (2004) The mechanisms by which family 10 glycoside hydrolases bind decorated substrates. J Biol Chem 279(10):9597–9605. https://doi.org/10.1074/jbc.M312278200
Porebski BT, Buckle AM (2016) Consensus protein design. Protein Eng Des Sel 29(7):245–251. https://doi.org/10.1093/protein/gzw015
Qin Z, Chen Q, Lin S, Luo S, Qiu Y, Zhao L (2018) Expression and characterization of a novel cold-adapted chitosanase suitable for chitooligosaccharides controllable preparation. Food Chem 253:139–147. https://doi.org/10.1016/j.foodchem.2018.01.137
Sheng J, Ji X, Yuan Z, Wang Z, Mi S (2015) Improvement in the thermostability of chitosanase from Bacillus ehimensis by introducing artificial disulfide bonds. Biotechnol Lett 38(10):1809–1815. https://doi.org/10.1007/s10529-016-2168-2
Sunagawa S, Coelho LP, Chaffron S, Kultima JR, Labadie K, Salazar G, Djahanschiri B, Zeller G, Mende DR, Alberti A, Cornejo-Castillo FM, Costea PI, Cruaud C, d'Ovidio F, Engelen S, Ferrera I, Gasol JM, Guidi L, Hildebrand F, Kokoszka F, Lepoivre C, Lima-Mendez G, Poulain J, Poulos BT, Royo-Llonch M, Sarmento H, Vieira-Silva S, Dimier C, Picheral M, Searson S, Kandels-Lewis S, Bowler C, de Vargas C, Gorsky G, Grimsley N, Hingamp P, Iudicone D, Jaillon O, Not F, Ogata H, Pesant S, Speich S, Stemmann L, Sullivan MB, Weissenbach J, Wincker P, Karsenti E, Raes J, Acinas SG, Bork P (2015) Ocean plankton. Structure and function of the global ocean microbiome. Science 348(6237):1261359. https://doi.org/10.1126/science.1261359
Thadathil N, Velappan SP (2014) Recent developments in chitosanase research and its biotechnological applications: a review. Food Chem 150:392–399. https://doi.org/10.1016/j.foodchem.2013.10.083
Tian J, Wu N, Guo X, Guo J, Zhang J, Fan Y (2007) Predicting the phenotypic effects of non-synonymous single nucleotide polymorphisms based on support vector machines. BMC Bioinformatics 8:450. https://doi.org/10.1186/1471-2105-8-450
Tian J, Wang P, Gao S, Chu X, Wu N, Fan Y (2010) Enhanced thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 by rational engineering of a glycine to proline mutation. FEBS J 277(23):4901–4908. https://doi.org/10.1111/j.1742-4658.2010.07895.x
Whitman WB, Coleman Dc Fau-Wiebe WJ, Wiebe WJ (1998) Prokaryotes: the unseen majority. Proc Natl Acad Sci U S A 95(12):6578–6583. https://doi.org/10.1073/pnas.95.12.6578
Xue Z, Yu Z, Wang T, Xuan G, Jing L, Sun Y, Li X (2016) The use of chitooligosaccharide in beer brewing for protection against beer-spoilage bacteria and its influence on beer performance. Biotechnol Lett 38(4):629–635. https://doi.org/10.1007/s10529-015-2013-z
Yin H, Fretté XC, Christensen LP, Grevsen K (2012) Chitosan oligosaccharides promote the content of polyphenols in Greek oregano (Origanum vulgare ssp. hirtum). J Agr Food Chem 60(1):136–143. https://doi.org/10.1021/jf204376j
Yin H, Du Y, Dong Z (2016) Chitin oligosaccharide and chitosan oligosaccharide: two similar but different plant elicitors. Front Plant Sci 7:522. https://doi.org/10.3389/fpls.2016.00522
Zhang J, Cao H, Li S, Zhao Y, Wang W, Xu Q, Du Y, Yin H (2015) Characterization of a new family 75 chitosanase from Aspergillus sp W-2. Int J Biol Macromol 81(11):362–369. https://doi.org/10.1016/j.ijbiomac.2015.08.026
Zhou W, Yuan H, Wang J, Yao J (2010) Production, purification and characterization of chitosanase produced by Gongronella sp. JG. Lett Appl Microbiol 46(1):49–54. https://doi.org/10.1111/j.1472-765X.2007.02262.x
Zhou Z, Zhao S, Wang S, Li X, Su L, Ma Y, Li J, Song J (2015) Extracellular overexpression of chitosanase from Bacillus sp. TS in Escherichia coli. Appl Biochem Biotech 175(7):3271–3286. https://doi.org/10.1007/s12010-015-1494-5
Zhou Y, Chen X, Li X, Han Y, Wang Y, Yao R, Li S (2019) Purification and characterization of a new cold-adapted and thermo-tolerant chitosanase from marine bacterium Pseudoalteromonas sp. SY39. Molecules (Basel, Switzerland) 24(1):E183. https://doi.org/10.3390/molecules24010183
Acknowledgments
We thank Dr. Lida Han in Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, for helping us to conduct the LC–QTOF-MS experiments, Prof. Yuhong Zhang for the TLC, and Prof. Bin Yao for Tm determination.
Funding
This study was funded by the Fundamental Research Funds for Central Non-profit Scientific Institution (Grant no. Y2019XK01), Central Public-Interest Scientific Institution Basal Research Fund (Grant no. Y2019XK19), and Freshwater Aquaculture Innovation Team Construction Project of Hebei Modern Agricultural Industry Technology System (HBCT2018180206).
Author information
Authors and Affiliations
Contributions
Jian Tian and Ningfeng Wu conceived and designed the research. Yanshuo Han and Feifei Guan conducted experiments. Jilu Sun contributed new reagents or analytical tools. Jian Tian and Feifei Guan analyzed data. Feifei Guan and Jian Tian wrote the manuscript. All authors read and approved the manuscript.
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Ethical statement
This article does not contain any studies with human participants or animals performed by any of the authors.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(PDF 366 kb)
Rights and permissions
About this article
Cite this article
Han, Y., Guan, F., Sun, J. et al. Identification of a chitosanase from the marine metagenome and its molecular improvement based on evolution data. Appl Microbiol Biotechnol 104, 6647–6657 (2020). https://doi.org/10.1007/s00253-020-10715-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00253-020-10715-8