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Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum

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Abstract

Type II arabinogalactan (AG) is a soluble prebiotic fiber stimulating the proliferation of bifidobacteria in the human gut. Larch AG, which is comprised of type II AG, is known to be utilized as an energy source for Bifidobacterium longum subsp. longum (B. longum). We have previously characterized GH43_24 exo-β-1,3-galactanase (Bl1,3Gal) for the degradation of type II AG main chains in B. longum JCM1217. In this study, we characterized GH30_5 exo-β-1,6-galactobiohydrolase (Bl1,6Gal) and GH43_22 α-l-arabinofuranosidase (BlArafA), which are degradative enzymes for type II AG side chains in cooperation with exo-β-1,3-galactanase. The recombinant exo-β-1,6-galactobiohydrolase specifically released β-1,6-galactobiose (β-1,6-Gal2) from the nonreducing terminal of β-1,6-galactooligosaccharides, and the recombinant α-l-arabinofuranosidase released arabinofuranose (Araf) from α-1,3-Araf-substituted β-1,6-galactooligosaccharides. β-1,6-Gal2 was additively released from larch AG by the combined use of type II AG degradative enzymes, including Bl1,3Gal, Bl1,6Gal, and BlArafA. The gene cluster encoding the type II AG degradative enzymes is conserved in all B. longum strains, but not in other bifidobacterial species. The degradative enzymes for type II AG side chains are thought to be important for the acquisition of type II AG in B. longum.

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References

  • Aalbers F, Turkenburg JP, Davies GJ, Dijkhuizen L, Lammerts van Bueren A (2015) Structural and functional characterization of a novel family GH115 4-O-methyl-α-glucuronidase with specificity for decorated arabinogalactans. J Mol Biol 427:3935–3946

    Article  CAS  PubMed  Google Scholar 

  • Amaretti A, Bernardi T, Leonardi A, Raimondi S, Zanoni S, Rossi M (2013) Fermentation of xylo-oligosaccharides by Bifidobacterium adolescentis DSMZ 18350: kinetics, metabolism, and β-xylosidase activities. Appl Microbiol Biotechnol 97:3109–3117

    Article  CAS  PubMed  Google Scholar 

  • Aspeborg H, Coutinho PM, Wang Y, Brumer H, Henrissat B (2012) Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 12:186

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bourgois TM, Van Craeyveld V, Van Campenhout S, Courtin CM, Delcour JA, Robben J, Volckaert G (2007) Recombinant expression and characterization of XynD from Bacillus subtilis subsp. subtilis ATCC 6051: a GH 43 arabinoxylan arabinofuranohydrolase. Appl Microbiol Biotechnol 75:1309–1317

    Article  CAS  PubMed  Google Scholar 

  • Brillouet J-M, Williams P, Will F, Müller G, Pellerina P (1996) Structural characterization of an apple juice arabinogalactan-protein which aggregates following enzymic dearabinosylation. Carbohydr Polym 29:271–275

    Article  CAS  Google Scholar 

  • Calame W, Weseler AR, Viebke C, Flynn C, Siemensma AD (2008) Gum arabic establishes prebiotic functionality in healthy human volunteers in a dose-dependent manner. Br J Nutr 100:1269–1275

    Article  CAS  PubMed  Google Scholar 

  • Cartmell A, McKee L, Pena MJ, Larsbrink J, Brumer H, Kaneko S, Ichinose H, Lewis RJ, Vikso-Nielsen A, Gilbert HJ, Marles-Wright J (2011) The structure and function of an arabinan-specific α-1,2-arabinofuranosidase identified from screening the activities of bacterial GH43 glycoside hydrolases. J Biol Chem 286:15483–15495

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cassab GI (1986) Arabinogalactan proteins during the development of soybean root nodules. Planta 168:441–446

    Article  CAS  PubMed  Google Scholar 

  • Crociani F, Alessandrini A, Mucci MM, Biavati B (1994) Degradation of complex carbohydrates by Bifidobacterium spp. Int J Food Microbiol 24:199–210

    Article  CAS  PubMed  Google Scholar 

  • Dubois M, Gilles KA, Hamilton JK, Rebers PA, Smith F (1956) Colorimetric method for determination of sugars and related substances. Anal Chem 28:350–356

    Article  CAS  Google Scholar 

  • Ficko-Blean E, Stuart CP, Suits MD, Cid M, Tessier M, Woods RJ, Boraston AB (2012) Carbohydrate recognition by an architecturally complex α-N-acetylglucosaminidase from Clostridium perfringens. PLoS One 7:e33524

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujimoto Z, Kuno A, Kaneko S, Kobayashi H, Kusakabe I, Mizuno H (2002) Crystal structures of the sugar complexes of Streptomyces olivaceoviridis E-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module. J Mol Biol 316:65–78

    Article  CAS  PubMed  Google Scholar 

  • Fujita K, Oura F, Nagamine N, Katayama T, Hiratake J, Sakata K, Kumagai H, Yamamoto K (2005) Identification and molecular cloning of a novel glycoside hydrolase family of core 1 type O-glycan-specific endo-α-N-acetylgalactosaminidase from Bifidobacterium longum. J Biol Chem 280:37415–37422

    Article  CAS  PubMed  Google Scholar 

  • Fujita K, Sakamoto S, Ono Y, Wakao M, Suda Y, Kitahara K, Suganuma T (2011) Molecular cloning and characterization of a β-L-arabinobiosidase in Bifidobacterium longum that belongs to a novel glycoside hydrolase family. J Biol Chem 286:5143–5150

    Article  CAS  PubMed  Google Scholar 

  • Fujita K, Sakaguchi T, Sakamoto A, Shimokawa M, Kitahara K (2014a) Bifidobacterium longum subsp. longum exo-β-1,3-galactanase, an enzyme for the degradation of type II arabinogalactan. Appl Environ Microbiol 80:4577–4584

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fujita K, Takashi Y, Obuchi E, Kitahara K, Suganuma T (2014b) Characterization of a novel β-L-arabinofuranosidase in Bifidobacterium longum: functional elucidation of a DUF1680 protein family member. J Biol Chem 289:5240–5249

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gavini F, Cayuela C, Antoine J-M, Lecoq C, Lefebvre B, Membré J-M, Neut C (2009) Differences in the distribution of Bifidobacterial and Enterobacterial species in human faecal microflora of three different (children, adults, elderly) age groups. Microb Ecol Health Dis 13:40–45

    Article  Google Scholar 

  • Göllner EM, Blaschek W, Classen B (2010) Structural investigations on arabinogalactan-protein from wheat, isolated with Yariv reagent. J Agric Food Chem 58:3621–3626

    Article  CAS  PubMed  Google Scholar 

  • Holmes EW, O’Brien JS (1979) Separation of glycoprotein-derived oligosaccharides by thin-layer chromatography. Anal Biochem 93:167–170

    Article  CAS  PubMed  Google Scholar 

  • Ichinose H, Kotake T, Tsumuraya Y, Kaneko S (2008a) Characterization of an endo-β-1,6-galactanase from Streptomyces avermitilis NBRC14893. Appl Environ Microbiol 74:2379–2383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ichinose H, Yoshida M, Fujimoto Z, Kaneko S (2008b) Characterization of a modular enzyme of exo-1,5-α-L-arabinofuranosidase and arabinan binding module from Streptomyces avermitilis NBRC14893. Appl Microbiol Biotechnol 80:399–408

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jiang D, Fan J, Wang X, Zhao Y, Huang B, Liu J, Zhang XC (2012) Crystal structure of 1,3Gal43A, an exo-β-1,3-galactanase from Clostridium thermocellum. J Struct Biol 180:447–457

    Article  CAS  PubMed  Google Scholar 

  • Kaneko S, Arimoto M, Ohba M, Kobayashi H, Ishii T, Kusakabe I (1998) Purification and substrate specificities of two α-L-arabinofuranosidases from Aspergillus awamori IFO 4033. Appl Environ Microbiol 64:4021–4027

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kato K, Odamaki T, Mitsuyama E, Sugahara H, Xiao JZ, Osawa R (2017) Age-related changes in the composition of gut Bifidobacterium species. Curr Microbiol 74:987–995

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawabata Y, Kaneko S, Kusakabe I, Gama Y (1995) Synthesis of regioisomeric methyl α-L-arabinofuranobiosides. Carbohydr Res 267:39–47

    Article  CAS  PubMed  Google Scholar 

  • Kelly GS (1999) Larch arabinogalactan: clinical relevance of a novel immune-enhancing polysaccharide. Altern Med Rev 4:96–103

    CAS  PubMed  Google Scholar 

  • Kotake T, Kaneko S, Kubomoto A, Haque MA, Kobayashi H, Tsumuraya Y (2004) Molecular cloning and expression in Escherichia coli of a Trichoderma viride endo-β-(1→6)-galactanase gene. Biochem J 377:749–755

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Luonteri E, Laine C, Uusitalo S, Teleman A, Siika-aho M, Tenkanen M (2003) Purification and characterization of Aspergillus β-D-galactanases acting on β-1,4- and β-1,3/6-linked arabinogalactans. Carbohydr Polym 53:155–168

    Article  CAS  Google Scholar 

  • Mewis K, Lenfant N, Lombard V, Henrissat B (2016) Dividing the large glycoside hydrolase family 43 into subfamilies: a motivation for detailed enzyme characterization. Appl Environ Microbiol 82:1686–1692

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nie S-P, Wang C, Cui SW, Wang Q, Xie M-Y, Phillips GO (2013) A further amendment to the classical core structure of gum arabic (Acacia senegal). Food Hydrocoll 31:42–48

    Article  CAS  Google Scholar 

  • Odonmažig P, Ebringerová A, Machová E, Alföldi J (1994) Structural and molecular properties of the arabinogalactan isolated from Mongolian larchwood (Larix dahurica L.). Carbohydr Res 252:317–324

    Article  PubMed  Google Scholar 

  • Okawa M, Fukamachi K, Tanaka H, Sakamoto T (2013) Identification of an exo-β-1,3-D-galactanase from Fusarium oxysporum and the synergistic effect with related enzymes on degradation of type II arabinogalactan. Appl Microbiol Biotechnol 97:9685–9694

    Article  CAS  PubMed  Google Scholar 

  • Ozaki S, Oki N, Suzuki S, Kitamura S (2010) Structural characterization and hypoglycemic effects of arabinogalactan-protein from the tuberous cortex of the white-skinned sweet potato (Ipomoea batatas L.). J Agric Food Chem 58:11593–11599

    Article  CAS  PubMed  Google Scholar 

  • Parche S, Amon J, Jankovic I, Rezzonico E, Beleut M, Barutçu H, Schendel I, Eddy MP, Burkovski A, Arigoni F, Titgemeyer F (2007) Sugar transport systems of Bifidobacterium longum NCC2705. J Mol Microbiol Biotechnol 12:9–19

    Article  CAS  PubMed  Google Scholar 

  • Ponder GR, Richards GN (1997) Arabinogalactan from Western larch, part III: alkaline degradation revisited, with novel conclusions on molecular structure. Carbohydr Polym 34:251–261

    Article  CAS  Google Scholar 

  • Sakamoto T, Taniguchi Y, Suzuki S, Ihara H, Kawasaki H (2007) Characterization of Fusarium oxysporum β-1,6-galactanase, an enzyme that hydrolyzes larch wood arabinogalactan. Appl Environ Microbiol 73:3109–3112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Saulnier L, Brillouet J-M, Moutounet M, du Penhoat CH, Michon V (1992) New investigations of the structure of grape arabino-galactan-protein. Carbohydr Res 224:219–235

    Article  CAS  PubMed  Google Scholar 

  • Shimoda R, Okabe K, Kotake T, Matsuoka K, Koyama T, Tryfona T, Liang HC, Dupree P, Tsumuraya Y (2014) Enzymatic fragmentation of carbohydrate moieties of radish arabinogalactan-protein and elucidation of the structures. Biosci Biotechnol Biochem 78:818–831

    Article  CAS  PubMed  Google Scholar 

  • Shinozaki A, Kawakami T, Hosokawa S, Sakamoto T (2014) A novel GH43 α-L-arabinofuranosidase of Penicillium chrysogenum that preferentially degrades single-substituted arabinosyl side chains in arabinan. Enzym Microb Technol 58-59:80–86

    Article  CAS  Google Scholar 

  • Shinozaki A, Hosokawa S, Nakazawa M, Ueda M, Sakamoto T (2015) Identification and characterization of three Penicillium chrysogenum α-L-arabinofuranosidases (PcABF43B, PcABF51C, and AFQ1) with different specificities toward arabino-oligosaccharides. Enzym Microb Technol 73-74:65–71

    Article  CAS  Google Scholar 

  • Smogyi M (1952) Notes on sugar determination. J Biol Chem 195:19–23

    CAS  PubMed  Google Scholar 

  • St John FJ, González JM, Pozharski E (2010) Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups. FEBS Lett 584:4435–4441

    Article  CAS  PubMed  Google Scholar 

  • Suzuki R, Wada J, Katayama T, Fushinobu S, Wakagi T, Shoun H, Sugimoto H, Tanaka A, Kumagai H, Ashida H, Kitaoka M, Yamamoto K (2008) Structural and thermodynamic analyses of solute-binding protein from Bifidobacterium longum specific for core 1 disaccharide and lacto-N-biose I. J Biol Chem 283:13165–13173

    Article  CAS  PubMed  Google Scholar 

  • Takata R, Tokita K, Mori S, Shimoda R, Harada N, Ichinose H, Kaneko S, Igarashi K, Samejima M, Tsumuraya Y, Kotake T (2010) Degradation of carbohydrate moieties of arabinogalactan-proteins by glycoside hydrolases from Neurospora crassa. Carbohydr Res 345:2516–2522

    Article  CAS  PubMed  Google Scholar 

  • ter Beek J, Guskov A, Slotboom DJ (2014) Structural diversity of ABC transporters. J Gen Physiol 143:419–435

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Terpend K, Possemiers S, Daguet D, Marzorati M (2013) Arabinogalactan and fructo-oligosaccharides have a different fermentation profile in the Simulator of the Human Intestinal Microbial Ecosystem (SHIME (R)). Environ Microbiol Rep 5:595–603

    Article  CAS  PubMed  Google Scholar 

  • Tryfona T, Liang HC, Kotake T, Tsumuraya Y, Stephens E, Dupree P (2012) Structural characterization of Arabidopsis leaf arabinogalactan polysaccharides. Plant Physiol 160:653–666

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tsumuraya Y, Hashimoto Y, Yamamoto S, Shibuya N (1984) Structure of L-arabino-D-galactan-containing glycoproteins from radish leaves. Carbohydr Res 134:215–228

    Article  CAS  Google Scholar 

  • Tsumuraya Y, Ogura K, Hashimoto Y, Mukoyama H, Yamamoto S (1988) Arabinogalactan-proteins from primary and mature roots of radish (Raphanus sativus L.). Plant Physiol 86:155–160

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van den Broek LA, Lloyd RM, Beldman G, Verdoes JC, McCleary BV, Voragen AG (2005) Cloning and characterization of arabinoxylan arabinofuranohydrolase-D3 (AXHd3) from Bifidobacterium adolescentis DSM20083. Appl Microbiol Biotechnol 67:641–647

    Article  CAS  PubMed  Google Scholar 

  • van den Broek LA, Hinz SW, Beldman G, Vincken JP, Voragen AG (2008) Bifidobacterium carbohydrases—their role in breakdown and synthesis of (potential) prebiotics. Mol Nutr Food Res 52:146–163

    Article  CAS  PubMed  Google Scholar 

  • Wada J, Ando T, Kiyohara M, Ashida H, Kitaoka M, Yamaguchi M, Kumagai H, Katayama T, Yamamoto K (2008) Bifidobacterium bifidum lacto-N-biosidase, a critical enzyme for the degradation of human milk oligosaccharides with a type 1 structure. Appl Environ Microbiol 74:3996–4004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yang L, Connaris H, Potter JA, Taylor GL (2015) Structural characterization of the carbohydrate-binding module of NanA sialidase, a pneumococcal virulence factor. BMC Struct Biol 15:15

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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This work was supported in part by JSPS KAKENHI Grant-in-Aid for Scientific Research (C), Grant Number 24580144.

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Correspondence to Kiyotaka Fujita.

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Fujita, K., Sakamoto, A., Kaneko, S. et al. Degradative enzymes for type II arabinogalactan side chains in Bifidobacterium longum subsp. longum. Appl Microbiol Biotechnol 103, 1299–1310 (2019). https://doi.org/10.1007/s00253-018-9566-4

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