Advertisement

Chitin/Chitosan-Active Enzymes Involved in Plant–Microbe Interactions

  • Tamo FukamizoEmail author
  • S. Shinya
Chapter
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 1142)

Abstract

Plant chitinase hydrolyzing β-1,4-glycosidic linkages of chitin are major enzymes acting in plant–microbe interactions and are involved in self-defense against fungal pathogens. Chitosanases from soil bacteria are also involved in plant defense by hydrolyzing chitosan components of the fungal cell wall. The crystal structures of these enzymes in complex with their substrates have been solved, and the mechanisms of substrate binding were elucidated at the atomic level. These findings enabled us to speculate on the enzyme targets under physiological conditions, leading us to define the physiological roles of the enzymes. The structures and functions of chitin/chitosan-binding modules appended to modular chitinases/chitosanases were analyzed by NMR and isothermal titration calorimetry (ITC), and the enzymes were found to form an appropriate modular organization to fulfill their roles in plant–microbe interactions.

Keywords

Chitinase Chitosanase Crystal structure Nuclear magnetic resonance Isothermal titration calorimetry 

Abbreviations

GlcNAc

2-acetamido-2-deoxy-D-glucopyranose

(GlcNAc)n

β-1,4-linked oligosaccharide of GlcNAc with a polymerization degree of n

GlcN

2-amino-2-deoxy-D-glucopyranose

(GlcN)n

β-1,4-linked oligosaccharide of GlcN with a polymerization degree of n

ITC

isothermal titration calorimetry

NMR

nuclear magnetic resonance

References

  1. Amon P, Haas E, Sumper M (1998) The sex-inducing pheromone and wounding trigger the same set of genes in the multicellular green alga Volvox. Plant Cell 10:781–789Google Scholar
  2. Andersen MD, Jensen A, Robertus JD, Leah R, Skriver K (1997) Heterologous expression and characterization of wild-type and mutant forms of a 26 kDa endochitinase from barley (Hordeum vulgare L.). Biochem J 322:815–822Google Scholar
  3. Arakane Y, Taira T, Ohnuma T, Fukamizo T (2012) Chitin-related enzymes in agro-biosciences. Curr Drug Targets 13:442–470Google Scholar
  4. Armenta S, Moreno-Mendieta S, Sánchez-Cuapio Z, Sánchez S, Rodríguez-Sanoja R (2017) Advances in molecular engineering of carbohydrate-binding modules. Proteins 85:1602–1617Google Scholar
  5. Baker LG, Specht CA, Donlin MJ, Lodge JK (2007) Chitosan, the deacetylated form of chitin, is necessary for cell wall integrity in Cryptococcus neoformans. Eukaryot Cell 6:855–867Google Scholar
  6. Bokma E, Rozeboom HJ, Sibbald M, Dijkstra BW, Beintema JJ (2002) Expression and characterization of active site mutants of hevamine, a chitinase from the rubber tree Hevea brasiliensis. Eur J Biochem 269:893–901Google Scholar
  7. Boraston AB, Bolam DN, Gilbert HJ, Davies GJ (2004) Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem J 382:769–781Google Scholar
  8. Boucher I, Fukamizo T, Honda Y, Willick GE, Neugebauer WA, Brzezinski R (1995) Site-directed mutagenesis of evolutionary conserved carboxylic amino acids in the chitosanase from Streptomyces sp. N174 reveals two residues essential for catalysis. J Biol Chem 270:31077–31082Google Scholar
  9. Broekaert WF, Mariën W, Terras FR, De Bolle MF, Proost P, Van Damme J, Dillen L, Claeys M, Rees SB, Vanderleyden J et al (1992) Antimicrobial peptides from Amaranthus caudatus seeds with sequence homology to the cysteine/glycine-rich domain of chitin-binding proteins. Biochemistry 31:4308–4314Google Scholar
  10. Brogue K, Chet I, Holliday M, Cressman R, Biddle P, Knowlton S, Mauvais CJ, Broglie R (1991) Transgenic plants with enhanced resistance to the fungal pathogen Rhizoctonia solani. Science 254:1194–1197Google Scholar
  11. Davies GJ, Wilson KS, Henrissat B (1997) Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem J 321:557–559Google Scholar
  12. Davis LL, Bartnicki-Garcia S (1984) Chitosan synthesis by the tandem action of chitin synthetase and chitin deacetylase from Mucor rouxii. Biochemistry 23:1065–1073Google Scholar
  13. Desaki Y, Miyata K, Suzuki M, Shibuya N, Kaku H (2018) Plant immunity and symbiosis signaling mediated by LysM receptors. Innate Immun 24:92–100Google Scholar
  14. El Hadrami A, Adam LR, El Hadrami I, Daayf F (2010) Chitosan in plant protection. Mar Drugs 8:968–987Google Scholar
  15. Fukamizo T, Honda Y, Goto S, Boucher I, Brzezinski R (1995) Reaction mechanism of chitosanase from Streptomyces sp. N174. Biochem J 311:377–383Google Scholar
  16. Fukamizo T, Juffer AH, Vogel HJ, Honda Y, Tremblay H, Boucher I, Neugebauer WA, Brzezinski R (2000) Theoretical calculation of pKa reveals an important role of Arg205 in the activity and stability of Streptomyces sp. N174 chitosanase. J Biol Chem 275:25633–25640Google Scholar
  17. Goormachtig S, Lievens S, Van de Velde W, Van Montagu M, Holsters M (1998) Srchi13, a novel early nodulin from Sesbania rostrata, is related to acidic class III chitinases. Plant Cell. 10:905–915Google Scholar
  18. Hart PJ, Monzingo AF, Ready MP, Ernst SR, Robertus JD (1993) Crystal structure of an endochitinase from Hordeum vulgare L. seeds. J Mol Biol 229:189–193Google Scholar
  19. Inamine S, Onaga S, Ohnuma T, Fukamizo T, Taira T (2015) Purification, cDNA cloning, and characterization of LysM-containing plant chitinase from horsetail (Equisetum arvense). Biosci Biotechnol Biochem 79:1296–1304Google Scholar
  20. Jiménez-Barbero J, Javier Cañada F, Asensio JL, Aboitiz N, Vidal P, Canales A, Groves P, Gabius HJ, Siebert HC (2006) Hevein domains: an attractive model to study carbohydrate-protein interactions at atomic resolution. Adv Carbohydr Chem Biochem 60:303–354Google Scholar
  21. Kasprzewska A (2003) Plant chitinases–regulation and function. Cell Mol Biol Lett 8:809–824Google Scholar
  22. Katsumi T, Lacombe-Harvey ME, Tremblay H, Brzezinski R, Fukamizo T (2005) Role of acidic amino acid residues in chitooligosaccharide-binding to Streptomyces sp. N174 chitosanase. Biochem Biophys Res Commun 338:1839–1844Google Scholar
  23. Kezuka Y, Kojima M, Mizuno R, Suzuki K, Watanabe T, Nonaka T (2010) Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering. Proteins 78:2295–2305Google Scholar
  24. Kitaoku Y, Fukamizo T, Numata T, Ohnuma T (2017) Chitin oligosaccharide binding to the lysin motif of a novel type of chitinase from the multicellular green alga, Volvox carteri. Plant Mol Biol 93:97–108Google Scholar
  25. Kitaoku Y, Nishimura S, Hirono T, Suginta W, Ohnuma T, Fukamizo T. (2019) Structures and chitin binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri. Glycobiology, in pressGoogle Scholar
  26. Lacombe-Harvey ME, Fukamizo T, Gagnon J, Ghinet MG, Dennhart N, Letzel T, Brzezinski R (2009) Accessory active site residues of Streptomyces sp. N174 chitosanase: variations on a common theme in the lysozyme superfamily. FEBS J 276:857–869Google Scholar
  27. Kovrigin EL (2012) NMR line shapes and multi-state binding equilibria. J Biomol NMR 53:257–270Google Scholar
  28. Lacombe-Harvey MÈ, Fortin M, Ohnuma T, Fukamizo T, Letzel T, Brzezinski R (2013) A highly conserved arginine residue of the chitosanase from Streptomyces sp. N174 is involved both in catalysis and substrate binding. BMC Biochem 14:23Google Scholar
  29. Leah R, Tommerup H, Svendsen I, Mundy J (1991) Biochemical and molecular characterization of three barley seed proteins with antifungal properties. J Biol Chem 266:1564–1573Google Scholar
  30. Lyu Q, Wang S, Xu W, Han B, Liu W, Jones DN, Liu W (2014) Structural insights into the substrate-binding mechanism for a novel chitosanase. Biochem J 461:335–345Google Scholar
  31. Lyu Q, Shi Y, Wang S, Yang Y, Han B, Liu W, Jones DN, Liu W (2015) Structural and biochemical insights into the degradation mechanism of chitosan by chitosanase OU01. Biochim Biophys Acta 1850:1953–1961Google Scholar
  32. 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 3:155–162Google Scholar
  33. Mauch F, Hadwiger LA, Boller T (1988a) Antifungal hydrolases in pea tissue: i. purification and characterization of two chitinases and two beta-1,3-glucanases differentially regulated during development and in response to fungal infection. Plant Physiol 87:325–333Google Scholar
  34. Mauch F, Mauch-Mani B, Boller T (1988b) Antifungal hydrolases in pea tissue: ii. inhibition of fungal growth by combinations of chitinase and beta-1,3-Glucanase. Plant Physiol 88:936–942Google Scholar
  35. Melchers LS, Apotheker-de Groot M, van der Knaap JA, Ponstein AS, Sela-Buurlage MB, Bol JF, Cornelissen BJ, van den Elzen PJ, Linthorst HJ (1994) A new class of tobacco chitinases homologous to bacterial exo-chitinases displays antifungal activity. Plant J 5:469–480Google Scholar
  36. Monzingo AF, Marcotte EM, Hart PJ, Robertus JD (1996) Chitinases, chitosanases, and lysozymes can be divided into procaryotic and eucaryotic families sharing a conserved core. Nat Struct Biol 3:133–140Google Scholar
  37. Neuhaus JM, Fritig B, Linthorst HJM, Meins F, Mikkelsen JD, Ryals J (1996) A revised nomenclature for chitinase genes. Plant Mol Biol Rep 14:102–104Google Scholar
  38. Norberg AL, Karlsen V, Hoell IA, Bakke I, Eijsink VG, Sørlie M (2010) Determination of substrate binding energies in individual subsites of a family 18 chitinase. FEBS Lett 584:4581–4585Google Scholar
  39. Ohnuma T, Taira T, Yamagami T, Aso Y, Ishiguro M (2004) Molecular cloning, functional expression, and mutagenesis of cDNA encoding class I chitinase from rye (Secale cereale) seeds. Biosci Biotechnol Biochem 68:324–332Google Scholar
  40. Ohnuma T, Onaga S, Murata K, Taira T, Katoh E (2008) LysM domains from Pteris ryukyuensis chitinase-A: a stability study and characterization of the chitin-binding site. J Biol Chem 283:5178–5187Google Scholar
  41. Ohnuma T, Numata T, Osawa T, Mizuhara M, Vårum KM, Fukamizo T (2011a) Crystal structure and mode of action of a class V chitinase from Nicotiana tabacum. Plant Mol Biol 75:291–304Google Scholar
  42. Ohnuma T, Numata T, Osawa T, Mizuhara M, Lampela O, Juffer AH, Skriver K, Fukamizo T (2011b) A class V chitinase from Arabidopsis thaliana: gene responses, enzymatic properties, and crystallographic analysis. Planta 234:123–137Google Scholar
  43. Ohnuma T, Ohnuma T, Sørlie M, Fukuda T, Kawamoto N, Taira T, Fukamizo T (2011c) Chitin oligosaccharide binding to a family GH19 chitinase from the moss Bryum coronatum. FEBS J 278:3991–4001Google Scholar
  44. Ohnuma T, Numata T, Osawa T, Inanaga H, Okazaki Y, Shinya S, Kondo K, Fukuda T, Fukamizo T (2012) Crystal structure and chitin oligosaccharide-binding mode of a ‘loopful’ family GH19 chitinase from rye, Secale cereale, seeds. FEBS J 279:3639–3651Google Scholar
  45. Ohnuma T, Umemoto N, Kondo K, Numata T, Fukamizo T (2013) Complete subsite mapping of a “loopful” GH19 chitinase from rye seeds based on its crystal structure. FEBS Lett 587:2691–2697Google Scholar
  46. Ohnuma T, Umemoto N, Nagata T, Shinya S, Numata T, Taira T, Fukamizo T (2014) Crystal structure of a “loopless” GH19 chitinase in complex with chitin tetrasaccharide spanning the catalytic center. Biochim Biophys Acta 1844:793–802Google Scholar
  47. Ohnuma T, Taira T, Umemoto N, Kitaoku Y, Sørlie M, Numata T, Fukamizo T (2017) Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis. Biochem Biophys Res Commun 494:736–741Google Scholar
  48. Onaga S, Taira T (2008) A new type of plant chitinase containing LysM domains from a fern (Pteris ryukyuensis): roles of LysM domains in chitin binding and antifungal activity. Glycobiology 18:414–423Google Scholar
  49. Roberts WK, Selitrennikoff CP (1986) Isolation and partial characterization of two antifungal proteins from barley. Biochim Biophys Acta 880:161–170Google Scholar
  50. Saito A, Ooya T, Miyatsuchi D, Fuchigami H, Terakado K, Nakayama SY, Watanabe T, Nagata Y, Ando A (2009) Molecular characterization and antifungal activity of a family 46 chitosanase from Amycolatopsis sp. CsO-2. FEMS Microbiol Lett 293:79–84Google Scholar
  51. Sasaki C, Vårum KM, Itoh Y, Tamoi M, Fukamizo T (2006) Rice chitinases: sugar recognition specificities of the individual subsites. Glycobiology 16:1242–1250Google Scholar
  52. Schlumbaum A, Mauch F, Vogeli U, Boller T (1986) Plant chitinases are potent inhibitors of fungal growth. Nature 324:365–367Google Scholar
  53. Shinya S, Ohnuma T, Yamashiro R, Kimoto H, Kusaoke H, Anbazhagan P, Juffer AH, Fukamizo T (2013) The first identification of carbohydrate binding modules specific to chitosan. J Biol Chem 288:30042–30053Google Scholar
  54. Shinya S, Nishimura S, Kitaoku Y, Numata T, Kimoto H, Kusaoke H, Ohnuma T, Fukamizo T (2016) Mechanism of chitosan recognition by CBM32 carbohydrate-binding modules from a Paenibacillus sp. IK-5 chitosanase/glucanase. Biochem J 473:1085–1095Google Scholar
  55. Shinya S, Ghinet MG, Brzezinski R, Furuita K, Kojima C, Shah S, Kovrigin EL, Fukamizo T (2017) NMR line shape analysis of a multi-state ligand binding mechanism in chitosanase. J Biomol NMR 67:309–319Google Scholar
  56. Suzukawa K, Yamagami T, Ohnuma T, Hirakawa H, Kuhara S, Aso Y, Ishiguro M (2003) Mutational analysis of amino acid residues involved in catalytic activity of a family 18 chitinase from tulip bulbs. Biosci Biotechnol Biochem 67:341–346Google Scholar
  57. Taira T, Ohnuma T, Yamagami T, Aso Y, Ishiguro M, Ishihara M (2002) Antifungal activity of rye (Secale cereale) seed chitinases: the different binding manner of class I and class II chitinases to the fungal cell walls. Biosci Biotechnol Biochem 66:970–977Google Scholar
  58. Taira T, Toma N, Ishihara M (2005a) Purification, characterization, and antifungal activity of chitinases from pineapple (Ananas comosus) leaf. Biosci Biotechnol Biochem 69:189–196Google Scholar
  59. Taira T, Ohdomari A, Nakama N, Shimoji M, Ishihara M (2005b) Characterization and antifungal activity of gazyumaru (Ficus microcarpa) latex chitinases: both the chitin-binding and the antifungal activities of class I chitinase are reinforced with increasing ionic strength. Biosci Biotechnol Biochem 69:811–818Google Scholar
  60. Taira T, Hayashi H, Tajiri Y, Onaga S, Uechi G, Iwasaki H, Ohnuma T, Fukamizo T (2009) A plant class V chitinase from a cycad (Cycas revoluta): biochemical characterization, cDNA isolation, and posttranslational modification. Glycobiology 19:1452–1461Google Scholar
  61. Taira T, Fujiwara M, Dennhart N, Hayashi H, Onaga S, Ohnuma T, Letzel T, Sakuda S, Fukamizo T (2010) Transglycosylation reaction catalyzed by a class V chitinase from cycad, Cycas revoluta: a study involving site-directed mutagenesis, HPLC, and real-time ESI-MS. Biochim Biophys Acta 1804:668–675Google Scholar
  62. Takenaka Y, Nakano S, Tamoi M, Sakuda S, Fukamizo T (2009) Chitinase gene expression in response to environmental stresses in Arabidopsis thaliana: chitinase inhibitor allosamidin enhances stress tolerance. Biosci Biotechnol Biochem 73:1066–1071Google Scholar
  63. Terwisscha van Scheltinga AC, Kalk KH, Beintema JJ, Dijkstra BW (1994) Crystal structures of hevamine, a plant defence protein with chitinase and lysozyme activity, and its complex with an inhibitor. Structure. 2:1181–1189Google Scholar
  64. Terwisscha van Scheltinga AC, Armand S, Kalk KH, Isogai A, Henrissat B, Dijkstra BW (1995) Stereochemistry of chitin hydrolysis by a plant chitinase/lysozyme and X-ray structure of a complex with allosamidin: evidence for substrate assisted catalysis. Biochemistry 34:15619–15623Google Scholar
  65. Tremblay H, Yamaguchi T, Fukamizo T (2001) Brzezinski R. Mechanism of chitosanase-oligosaccharide interaction: subsite structure of Streptomyces sp. N174 chitosanase and the role of Asp57 carboxylate. J Biochem 130:679–686Google Scholar
  66. Umemoto N, Kanda Y, Ohnuma T, Osawa T, Numata T, Sakuda S, Taira T, Fukamizo T (2015a) Crystal structures and inhibitor binding properties of plant class V chitinases: the cycad enzyme exhibits unique structural and functional features. Plant J 82:54–66Google Scholar
  67. Umemoto N, Ohnuma T, Osawa T, Numata T, Fukamizo T (2015b) Modulation of the transglycosylation activity of plant family GH18 chitinase by removing or introducing a tryptophan side chain. FEBS Lett 589:2327–2333Google Scholar
  68. van Aalten DM, Komander D, Synstad B, Gåseidnes S, Peter MG, Eijsink VG (2001) Structural insights into the catalytic mechanism of a family 18 exo-chitinase. Proc Natl Acad Sci U S A 98:8979–8984Google Scholar
  69. Verburg JG, Huynh QK (1991) Purification and characterization of an antifungal chitinase from Arabidopsis thaliana. Plant Physiol 95:450–455Google Scholar
  70. Yang H, Zhang T, Masuda T, Lv C, Sun L, Qu G, Zhao G (2011) Chitinase III in pomegranate seeds (Punica granatum Linn.): a high-capacity calcium-binding protein in amyloplasts. Plant J 68:765–776Google Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2019

Authors and Affiliations

  1. 1.Biochemistry-Electrochemistry Research UnitSchool of Chemistry, Suranaree University of TechnologyNakhon RatchasimaThailand
  2. 2.Laboratory of Molecular BiophysicsInstitute of Protein Research, Osaka UniversityOsakaJapan

Personalised recommendations